Module Index

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This page provides a comprehensive list of modules available in QIT. The usage page of each module is also included for reference. Some of these modules are only available on the command line using the qit program, but most can be used interactively from qitview. We're planning to expand the documentation, but if you are wondering about a specific module, it would be helpful to send the developers a note so we know which modules need more work.

You can also get this list of modules by running:

qit --list

and if you want to see the documentation for a particular module you can run:

qit AffineCompose --help

This documentation is also available when you open the module in qitview.

Contents

AffineCompose

Name:

 AffineCompose

Description:

 Compose two affine transforms

Required Input Arguments:

 --inner <Affine>
   input inner
 --outer <Affine>
   input outer

Required Output Arguments:

 --output <Affine>
   output affine

Author:

 Ryan Cabeen

AffineConvert

Name:

 AffineConvert

Description:

 Convert an affine transform between file formats

Required Input Arguments:

 --input <Affine>
   input affine

Required Output Arguments:

 --output <Affine>
   output affine

Author:

 Ryan Cabeen

AffineCreate

Name:

 AffineCreate

Description:

 Create an affine transform based on user specified parameters

Optional Parameter Arguments:

 --xscale <double>
   scaling in x (Default: 1.0)
 --yscale <double>
   scaling in y (Default: 1.0)
 --zscale <double>
   scaling in z (Default: 1.0)
 --xtrans <double>
   translation in x (Default: 0.0)
 --ytrans <double>
   translation in y (Default: 0.0)
 --ztrans <double>
   translation in z (Default: 0.0)
 --xaxis <double>
   rotation axis in x (Default: 0.0)
 --yaxis <double>
   rotation axis in y (Default: 0.0)
 --zaxis <double>
   rotation axis in z (Default: 0.0)
 --angle <double>
   rotation angle (Default: 0.0)

Required Output Arguments:

 --output <Affine>
   output affine

Author:

 Ryan Cabeen

AffineInvert

Name:

 AffineInvert

Description:

 Invert an affine transform

Required Input Arguments:

 --input <Affine>
   input affine

Required Output Arguments:

 --output <Affine>
   output affine

Author:

 Ryan Cabeen

AffinePrintInfo

Name:

 AffinePrintInfo

Description:

 Print basic information about an affine transform

Required Input Arguments:

 --input <Affine>
   the input affine

Author:

 Ryan Cabeen

AffineReduce

Name:

 AffineReduce

Description:

 Reduce an affine transform to a simpler affine transform in one of several
 possible ways

Required Input Arguments:

 --input <Affine>
   an affine transform

Optional Parameter Arguments:

 --translation
   include the translation part
 --linear
   include the linear part
 --orthogonalize
   orthogonalize the linear part

Required Output Arguments:

 --output <Affine>
   output affine

Author:

 Ryan Cabeen

CurvesAttributes

Name:

 CurvesAttributes

Description:

 Manipulate curves vertex attributes.  Operations support comma-delimited
 lists

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --copy <String>
   copy attribute (x=y syntax)
 --rename <String>
   rename attribute (x=y syntax)
 --remove <String>
   remove attribute (- for all)
 --retain <String>
   retain the given attributes and remove others)

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesBox

Name:

 CurvesBox

Description:

 Compute a bounding box from curves

Required Input Arguments:

 --input <Curves>
   input curves

Required Output Arguments:

 --output <Solids>
   output box

Author:

 Ryan Cabeen

CurvesCat

Name:

 CurvesCat

Description:

 Concatenate curves files

Required Input Arguments:

 --input <File(s)>
   specify an input curves

Optional Parameter Arguments:

 --names <String(s)>
   use pattern-based input with the given names
 --label
   add a label attribute
 --attr <String>
   use a specific label attribute name (Default: label)

Required Output Arguments:

 --output <File>
   specify the output

Optional Output Arguments:

 --output-table <File>
   specify the output table name

Author:

 Ryan Cabeen

CurvesClusterFeature

Name:

 CurvesClusterFeature

Description:

 Cluster curves using simple curve features (length, endpoints, position,
 shape) using K-means

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --length
   include the length
 --endpoints
   include tensor product of endpoints
 --gaussian
   include the Gaussian shape
 --num <Integer>
   the number of clusters (Default: 2)
 --thresh <Double>
   the threshold size for clusters (enables DP-means)
 --iters <Integer>
   the maxima number of iterations (Default: 100)
 --restarts <Integer>
   the number of restarts
 --relabel
   relabel to reflect cluster size
 --largest
   keep only the largest cluster

Optional Output Arguments:

 --output <Curves>
   the output curves
 --protos <Curves>
   the prototypical curves for each cluster

Author:

 Ryan Cabeen

CurvesClusterGraph

Name:

 CurvesClusterGraph

Description:

 Curve bundle segmentation with graph-based thresholding

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --dist <String>
   the name of the inter-curve distance (Default: meanhaus)
 --thresh <double>
   the threshold for grouping (Default: 1.0)
 --largest
   retain the largest group
 --relabel
   relabel to reflect cluster size

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

Citation:

 Felzenszwalb, P. F., & Huttenlocher, D. P. (2004). Efficient graph-based
 image segmentation. International journal of computer vision, 59(2), 167-181.

CurvesClusterHierarchical

Name:

 CurvesClusterHierarchical

Description:

 Cluster curves with hierarchical clustering.

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --dist <String>
   the name of the inter-curve distance (Default: meanhaus)
 --num <Integer>
   the number of clusters
 --thresh <Double>
   the threshold for grouping
 --density <Double>
   resample the curves to speed up computation
 --epsilon <Double>
   simplify the curves to speed up computation
 --relabel
   relabel to reflect cluster size

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

Citation:

 Zhang, S., Correia, S., & Laidlaw, D. H. (2008). Identifying white-matter
 fiber bundles in DTI data using an automated proximity-based fiber-clustering
 method. IEEE transactions on visualization and computer graphics, 14(5),
 1044-1053.

CurvesClusterQuickBundle

Name:

 CurvesClusterQuickBundle

Description:

 Cluster curves with the quicksbundles algorithm

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --samples <Integer>
   the number of sample vertices (Default: 5)
 --thresh <Double>
   the separation threshold (Default: 1000.0)
 --relabel
   relabel to reflect cluster size

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

Citation:

 Garyfallidis, E., Brett, M., Correia, M. M., Williams, G. B., & Nimmo-Smith,
 I. (2012). Quickbundles, a method for tractography simplification. Frontiers
 in neuroscience, 6, 175.

CurvesClusterSpectral

Name:

 CurvesClusterSpectral

Description:

 Cluster curves with spectral clustering.

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --dist <String>
   the name of the inter-curve distance (Default: meanhaus)
 --num <Integer>
   the number of clusters
 --density <Double>
   resample the curves to speed up computation
 --epsilon <Double>
   simplify the curves to speed up computation
 --relabel
   relabel to reflect cluster size

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

Citation:

 Cluster curves with spectral clustering.  O'Donnell, L. J., & Westin, C. F.
 (2007). Automatic tractography segmentation using a high-dimensional white
 matter atlas. IEEE transactions on medical imaging, 26(11), 1562-1575.

CurvesCompare

Name:

 CurvesCompare

Description:

 Compare a pair of curves objects quantitatively

Required Input Arguments:

 --left <Curves>
   input curves
 --right <Curves>
   the other curves

Optional Parameter Arguments:

 --delta <double>
   the volume resolution (Default: 1.0)
 --thresh <double>
   the density threshold (Default: 0.5)

Required Output Arguments:

--output output table Author: Ryan Cabeen

CurvesCompare$1

 No module named CurvesCompare$1 was found!
 Maybe you are looking for one of these?
   CurvesCompare
   CurvesConvert
   CurvesSample
   CurvesNearest
   CurvesCrop
   CurvesSimplify
   CurvesCat
   CurvesMeasure
   CurvesFeatures
   CurvesRelabel

CurvesCompare$2

 No module named CurvesCompare$2 was found!
 Maybe you are looking for one of these?
   CurvesCompare
   CurvesConvert
   CurvesSample
   CurvesNearest
   CurvesCrop
   CurvesSimplify
   CurvesCat
   CurvesMeasure
   CurvesFeatures
   CurvesRelabel

CurvesConvert

Name:

 CurvesConvert

Description:

 Convert curves between file formats

Required Input Arguments:

 --input <Curves>
   input curves

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesCrop

Name:

 CurvesCrop

Description:

 Crop curves to retain only portions inside the selection

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Input Arguments:

 --mask <Mask>
   a mask
 --solids <Solids>
   some solids

Optional Parameter Arguments:

 --invert
   invert the selection
 --and
   require that curves are inside all solids (logical AND)

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesCull

Name:

 CurvesCull

Description:

 Cull redundant curves.  This can be done using SCPT (scpt) or pairwise
 distance-based clustering (haus, cham, end, or cutoff).  Distance based
 clustering is much slower but technically more accurate.

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --dist <String>
   the name of the inter-curve distance (scpt, haus, cham, end, or cutoff).
   Pairwise distances can be symmeterized by adding mean, min, or max to the
   name (except scpt). (Default: scpt)
 --thresh <Double>
   the threshold for removal in mm (but the exact meaning of this depends on
   the distance metric, so be careful) (Default: 1.5)

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

Citation:

 Zhang, S., Correia, S., & Laidlaw, D. H. (2008). Identifying white-matter
 fiber bundles in DTI data using an automated proximity-based fiber-clustering
 method. IEEE transactions on visualization and computer graphics, 14(5),
 1044-1053.

CurvesDensity

Name:

 CurvesDensity

Description:

 Compute a volumetric density of curves.  This works by find the voxels that
 intersect the curves and accumulating how many curves intersected each voxel.

Required Input Arguments:

 --input <Curves>
   input curves

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)

Optional Parameter Arguments:

 --unit
   normalize the density to unit value

Required Output Arguments:

 --output <Volume>
   output density volume

Author:

 Ryan Cabeen

CurvesEndpoints

Name:

 CurvesEndpoints

Description:

 Extract curve endpoints and return them as vects

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --head
   curve head vertices
 --tail
   curve tail vertices

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

CurvesExtract

Name:

 CurvesExtract

Description:

 Extract only curves that match a given attribute value

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --attr <String>
   the attribute name of the label used to select (Default: label)
 --which <String>
   which labels to extract, e.g. 1,2,3:5 (Default: )

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesFeatures

Name:

 CurvesFeatures

Description:

 Compute features of curves and add them as vertex attributes

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --tangent
   compute tangents
 --color
   compute vertex colors
 --arclength
   compute per-vertex arclength
 --index
   compute per-vertex index
 --fraction
   compute per-vertex fraction along curve
 --count
   compute per-curve vertex count
 --length
   compute per-curve length
 --frame
   compute the per-vertex frenet frame
 --curvature
   compute the per-vertex curvatures
 --density
   compute the per-vertex density
 --stats
   compute the per-curve statistics of vertex curvature and density
 --all
   compute all possible features
 --voxel <double>
   specify a voxel size used for computing density (Default: 1.0)

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesFeatures$1

 No module named CurvesFeatures$1 was found!
 Maybe you are looking for one of these?
   CurvesFeatures
   CurvesNearest
   CurvesMeasure
   CurvesVertices
   CurvesFilterSEV
   MeshFeatures
   CurvesReduce
   CurvesTubes
   CurvesSelect
   CurvesCompare

CurvesFeatures$2

 No module named CurvesFeatures$2 was found!
 Maybe you are looking for one of these?
   CurvesFeatures
   CurvesNearest
   CurvesMeasure
   CurvesVertices
   CurvesFilterSEV
   MeshFeatures
   CurvesReduce
   CurvesTubes
   CurvesSelect
   CurvesCompare

CurvesFilterKernel

Name:

 CurvesFilterKernel

Description:

 Filter curves with kernel regression.  This uses a non-parametric statistical
 approach to smooth the curves

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --density <Double>
   resample with a given vertex density (mm/vertex), otherwise the original
   arclength sampling is used
 --sigma <Double>
   use the given spatial bandwidth (Default: 4.0)
 --order <int>
   specify the order of the local approximating polynomial (Default: 2)
 --thresh <Double>
   the threshold for excluding data from local regression (Default: 0.05)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesFilterPolynomial

Name:

 CurvesFilterPolynomial

Description:

 Filter cures with polynomial splines

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --density <Double>
   resample with a given vertex density (mm/vertex), otherwise the original
   arclength sampling is used
 --lambda <Double>
   use regularization Tikhonov regularization (specify the negative log, so
   and input of 2.3 would give a regularization weight of 0.1)
 --order <Integer>
   use a given polynomial order (Default: 10)
 --residual
   save the residuals

Required Output Arguments:

 --output <Curves>
   output curves

Optional Output Arguments:

 --outputResiduals <Vects>
   output residual error between the polynomial and the curve

Author:

 Ryan Cabeen

CurvesFilterSEV$1

 No module named CurvesFilterSEV$1 was found!
 Maybe you are looking for one of these?
   CurvesFilterSEV
   CurvesFilterKernel
   CurvesFitPASCAL
   CurvesOutlierSCPT
   CurvesClusterSCPT
   CurvesFeatures
   CurvesSelect
   CurvesExtract
   CurvesConvert
   CurvesClusterGraph

CurvesFitPASCAL$1

 No module named CurvesFitPASCAL$1 was found!
 Maybe you are looking for one of these?
   CurvesFitPASCAL
   CurvesFilterSEV
   CurvesFilterKernel
   CurvesSelect
   CurvesMaskSelect
   CurvesOutlierSCPT
   CurvesClusterSCPT
   CurvesMath
   CurvesExtract
   CurvesCrop

CurvesFitPASCAL$2

 No module named CurvesFitPASCAL$2 was found!
 Maybe you are looking for one of these?
   CurvesFitPASCAL
   CurvesFilterSEV
   CurvesFilterKernel
   CurvesSelect
   CurvesMaskSelect
   CurvesOutlierSCPT
   CurvesClusterSCPT
   CurvesMath
   CurvesExtract
   CurvesCrop

CurvesLandmarks

Name:

 CurvesLandmarks

Description:

 Generate landmarks from curves using simplification and vertex clustering

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --subsamp <Integer>
   the number of curves to subsample (Default: 1000)
 --eps <Double>
   the spatial threshold for simplificaion (Default: 2.0)
 --radius <Double>
   the diameter of clusters for vertex grouping
 --num <Integer>
   the number of clusters to start with (Default: 2)

Required Output Arguments:

 --output <Vects>
   the output landmarks

Author:

 Ryan Cabeen

Citation:

 (in preparation)

CurvesLengths

Name:

 CurvesLengths

Description:

 Compute the lengths of the given curves

Required Input Arguments:

 --input <Curves>
   the input curves

Required Output Arguments:

 --output <Vects>
   the output landmarks

Author:

 Ryan Cabeen

CurvesMask

Name:

 CurvesMask

Description:

 Compute a volumetric mask of curves.  Any voxel that intersects the curves
 will be included

Required Input Arguments:

 --input <Curves>
   input curves

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)

Optional Parameter Arguments:

 --thresh <double>
   the threshold (Default: 0.5)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

CurvesMaskSelect

Name:

 CurvesMaskSelect

Description:

 Select curves using volumetric masks

Required Input Arguments:

 --input <Curves>
   input curves

Optional Input Arguments:

 --deform <Deformation>
   a deformation between curves and the masks
 --include <Mask>
   use an include mask (AND for multiple labels)
 --exclude <Mask>
   use an exclude mask
 --contain <Mask>
   use a containment mask

Optional Parameter Arguments:

 --binarize
   binarize the include mask
 --invert
   invert the exclude mask
 --skip
   skip masks without regions or an insufficient number of regions without
   error
 --thresh <Double>
   specify a containment threshold (Default: 0.8)
 --endpoints
   select based on only curve endpoints
 --connect
   select curves with endpoints that connect different labels

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesMaskSelectBatch

Name:

 CurvesMaskSelectBatch

Description:

 select curves from masks in batch mode

Required Input Arguments:

 --input <File>
   specify an input curves

Optional Input Arguments:

 --deform <File>
   specify a deformation between curves and volumes

Optional Parameter Arguments:

 --names <Spec>
   specify bundle identifiers
 --thresh <Value>
   specify threshold for containment
 --endpoints
   specify that only endpoints should be tested
 --invert
   specify masks should be inverted
 --binarize
   specify masks should be binarized
 --include <FilePattern>
   specify an filename pattern for an include mask
 --exclude <FilePattern>
   specify an filename pattern for an exclude mask
 --contain <FilePattern>
   specify an filename pattern for an contain mask

Required Output Arguments:

 --output <FilePattern>
   specify an output directory

Author:

 Ryan Cabeen

CurvesMath

Name:

 CurvesMath

Description:

 Evaluate a mathematical expression at each vertex of curves.

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: x > 0.5)
 --result <String>
   the attribute name for the result (Default: result)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesMeasure

Name:

 CurvesMeasure

Description:

 Measure statistics of curves and store the results in a table

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --delta <double>
   the volume resolution (Default: 1.0)
 --thresh <double>
   the density threshold (Default: 0.5)
 --advanced
   add advanced measures (outlier measures).  warning: these take polynomial
   time with the number of curves
 --neighbors <int>
   specify a number of neighbors for topographic measures (Default: 16)

Required Output Arguments:

--output
output table Author: Ryan Cabeen

CurvesMeasure$1

 No module named CurvesMeasure$1 was found!
 Maybe you are looking for one of these?
   CurvesMeasure
   CurvesFeatures
   CurvesNearest
   CurvesMask
   CurvesReduce
   CurvesSelect
   CurvesMaskSelect
   CurvesDensity
   CurvesCompare
   CurvesMath

CurvesMeasure$2

 No module named CurvesMeasure$2 was found!
 Maybe you are looking for one of these?
   CurvesMeasure
   CurvesFeatures
   CurvesNearest
   CurvesMask
   CurvesReduce
   CurvesSelect
   CurvesMaskSelect
   CurvesDensity
   CurvesCompare
   CurvesMath

CurvesMeasure$3

 No module named CurvesMeasure$3 was found!
 Maybe you are looking for one of these?
   CurvesMeasure
   CurvesFeatures
   CurvesNearest
   CurvesMask
   CurvesReduce
   CurvesSelect
   CurvesMaskSelect
   CurvesDensity
   CurvesCompare
   CurvesMath

CurvesMeasure$4

 No module named CurvesMeasure$4 was found!
 Maybe you are looking for one of these?
   CurvesMeasure
   CurvesFeatures
   CurvesNearest
   CurvesMask
   CurvesReduce
   CurvesSelect
   CurvesMaskSelect
   CurvesDensity
   CurvesCompare
   CurvesMath

CurvesMeasureBatch

Name:

 CurvesMeasureBatch

Description:

 Compute measures of a set of curves in batch mode.

Required Input Arguments:

 --input <FilePattern>
   specify an input bundle filename pattern

Optional Input Arguments:

 --volume <String=Volume> [...]
   specify volumes to sample
 --deform <File>
   specify a deformation between curves and volumes

Required Parameter Arguments:

 --names <Spec>
   specify bundle identifiers

Optional Parameter Arguments:

 --attrs <String> [<String>] [...]
   only include the specified attributes
 --param <String>
   compute statistics with parameterization attribute (discrete valued)
 --thresh <Double>
   specify a density threshold for volumetry (Default: 1.0)
 --delta <Double>
   specify a density threshold for volumetry (Default: 1.0)
 --neighbors <Integer>
   specify a number of neighbors for advanced metrics (Default: 1)
 --advanced
   include advanced metrics
 --interp <String>
   specify an interpolation method (Default: Nearest)

Required Output Arguments:

 --output <Directory>
   specify an output directory

Author:

 Ryan Cabeen

CurvesNearest

Name:

 CurvesNearest

Description:

 Extract the nearest curve to a collection

Required Input Arguments:

 --input <Curves>
   input curves
 --ref <Curves>
   reference curves

Optional Input Arguments:

 --deform <Deformation>
   a deformation for the input curve

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesOrient

Name:

 CurvesOrient

Description:

 Orient curves to best match endpoints, i.e. flip them to make the starts and
 ends as close as possible

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --iters <int>
   a maxima number of iterations (Default: 10)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesPrintInfo

Name:

 CurvesPrintInfo

Description:

 Print basic information about curves

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --stats
   print statistics
 --length
   print statistics of curve lengths

Author:

 Ryan Cabeen

CurvesPrototype

Name:

 CurvesPrototype

Description:

 Extract a prototypical curve that has maximum track density

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --delta <double>
   the volume resolution (Default: 1.0)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesReduce

Name:

 CurvesReduce

Description:

 Reduce the number of curves by random subsampling

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --count <Integer>
   a maxima number of curves (Default: 10000)

Required Output Arguments:

 --output <Curves>
   output selected curves

Author:

 Ryan Cabeen

CurvesRelabel

Name:

 CurvesRelabel

Description:

 Relabel curves from biggest to smallest cluster

Required Input Arguments:

 --input <Curves>
   the input curves

Required Parameter Arguments:

 --threshold <Double>
   retain only clusters above a given proportion of the total

Optional Parameter Arguments:

 --largest
   keep only the largest label

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesResample

Name:

 CurvesResample

Description:

 Resample the position of vertices along curves so that they have uniform
 spacing

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --num <Integer>
   resample with a constant number of vertices per curve (0 specifices that
   the max should be used)
 --density <Double>
   resample with a given vertex density (mm/vertex)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesSample

Name:

 CurvesSample

Description:

 Sample a volume at the vertices of curves

Required Input Arguments:

 --input <Curves>
   the input curves
 --volume <Volume>
   the volume

Optional Parameter Arguments:

 --interp <InterpolationType>
   interpolation method (Options: Nearest, Trilinear, Tricubic, Gaussian,
   GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)
 --attr <String>
   attribute name (Default: sampled)

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesSegmentAlongArclength

Name:

 CurvesSegmentAlongArclength

Description:

 Segment a bundle by matching vertices along its arclength based on a
 reference curve

Required Input Arguments:

 --input <Curves>
   the input curves
 --reference <Curves>
   input reference curve

Optional Input Arguments:

 --deform <Deformation>
   a deformation to transform the reference curves

Optional Parameter Arguments:

 --attr <String>
   an attribute name for the label (Default: label)
 --outlier <Double>
   remove outliers with a given probability threshold

Required Output Arguments:

 --output <Curves>
   the output curves

Author:

 Ryan Cabeen

CurvesSegmentAlongDistance

Name:

 CurvesSegmentAlongDistance

Description:

 Segment a bundle by matching vertices along its arclength based on a
 reference curve

Required Input Arguments:

 --input <Curves>
   the input curves
 --reference <Curves>
   input reference curve

Optional Input Arguments:

 --deform <Deformation>
   a deformation to transform the reference curves

Optional Parameter Arguments:

 --attr <String>
   an attribute name for the label (Default: label)
 --nearest
   segment the bundle based on the nearest input curve to the reference
 --delta <Double>
   the volume resolution (Default: 1.0)

Required Output Arguments:

 --output <Curves>
   the output curves

Optional Output Arguments:

 --dist <Volume>
   output distance volume
 --label <Volume>
   output label volume

Author:

 Ryan Cabeen

CurvesSelect

Name:

 CurvesSelect

Description:

 Select a which of curves using a number of possible criteria

Required Input Arguments:

 --input <Curves>
   input curves

Optional Input Arguments:

 --deform <Deformation>
   a deformation between curves and the masks
 --mask <Mask>
   a mask
 --solids <Solids>
   some solids
 --vects <Vects>
   some vects

Optional Parameter Arguments:

 --radius <double>
   vects radius (Default: 5.0)
 --or
   use OR (instead of AND) to combine selections
 --invert
   invert the selection after combining
 --exclude
   exclude the selected curves
 --endpoints
   select based on only curve endpoints
 --expression <String>
   select based on a boolean-valued expression using any of: length, size,
   min_attr, max_attr, mean_attr, or sum_attr
 --minlen <Double>
   a minimum length
 --maxlen <Double>
   a maximum length
 --longest
   select the longest curve

Required Output Arguments:

 --output <Curves>
   output selected curves

Author:

 Ryan Cabeen

CurvesSetAttributeLookupTable

Name:

 CurvesSetAttributeLookupTable

Description:

 Set vertex attributes of curves based on a table.  The curves should have a
 discrete-valued attribute that is used to match vertices to entries in the
 table.

Required Input Arguments:

 --curves <Curves>
   input curves
--table
input table Optional Input Arguments: --lookup
a lookup table to relate names to indices Optional Parameter Arguments: --merge <String> a field name to merge on (Default: name) --index <String> the table index field name (Default: index) --value <String> a table field to get (Default: value) --cindex <String> the curves index field name (defaults to table field name) --cvalue <String> a curves field to set (defaults to table field name) --background <double> a background value (Default: 0.0) --missing <Double> an missing value Required Output Arguments: --output <Curves> output curves Author: Ryan Cabeen

CurvesSetAttributeVects

Name:

 CurvesSetAttributeVects

Description:

 Set vertex attributes of curves based on a table.  The curves should have a
 discrete-valued attribute that is used to match vertices to entries in the
 table.

Required Input Arguments:

 --curves <Curves>
   input curves
 --vects <Vects>
   input vectors

Optional Parameter Arguments:

 --name <String>
   an attribute field name (Default: attr)
 --quiet
   don't complain if the vects and curves don't match (and try to add as much
   data to the curves as possible)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesSimplify

Name:

 CurvesSimplify

Description:

 Simplify curves with the Ramer-Douglas-Peucker algorithm

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Parameter Arguments:

 --epsilon <double>
   the distance threshold (Default: 2.0)
 --radial
   use radial distance

Required Output Arguments:

 --output <Curves>
   the output simplified curves

Author:

 Ryan Cabeen

Citation:

 Heckbert, Paul S.; Garland, Michael (1997). Survey of polygonal
 simplification algorithms

CurvesSmooth

Name:

 CurvesSmooth

Description:

 Smooth out irregularities in the input curves using laplacian (or Taubin)
 smoothing.  This works best if curve vertices are equally spaced along each
 curve.

Required Input Arguments:

 --input <Curves>
   input curves

Optional Parameter Arguments:

 --iters <int>
   number of iterations (Default: 1)
 --lambda <double>
   lambda smoothing parameter (Default: 0.3)
 --mu <Double>
   mu smoothing parameter (for Taubin smoothing)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesSplit

Name:

 CurvesSplit

Description:

 Split a curves file into multiple parts

Required Input Arguments:

 --input <File>
   specify an input curves file

Optional Input Arguments:

 --table <File>
   specify a table for looking up names

Optional Parameter Arguments:

 --attr <String>
   use a specific label attribute name (Default: label)
 --names <String(s)>
   specify a which of names to extract

Required Output Arguments:

 --output <Pattern>
   specify the output filename pattern with %s

Author:

 Ryan Cabeen

CurvesTransform

Name:

 CurvesTransform

Description:

 Apply a spatial transformation to curves

Required Input Arguments:

 --input <Curves>
   input curves

Optional Input Arguments:

 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm
 --pose <Volume>
   apply a transform to match the pose of a volume
 --invpose <Volume>
   apply a transform to match the inverse pose of a volume

Optional Parameter Arguments:

 --tx <Double>
   translate the curves in by the given about in the x dimension
 --ty <Double>
   translate the curves in by the given about in the y dimension
 --tz <Double>
   translate the curves in by the given about in the z dimension

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

CurvesTubes

Name:

 CurvesTubes

Description:

 Create a mesh representing 3D tubes based on the input curves

Required Input Arguments:

 --input <Curves>
   the input curves

Optional Input Arguments:

 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --color
   use per-vertex orientation coloring
 --wash <Double>
   the color wash (Default: 0.2)
 --dthick <Double>
   the default tube thickness (Default: 0.15)
 --fthick <Double>
   the tube thickness factor (scales the thickness attribute, it it is
   present) (Default: 1.0)
 --resolution <int>
   the tube resolution (Default: 5)
 --smooth
   create smooth tube caps (the default will use a separate disk for tube
   caps)

Required Output Arguments:

 --output <Mesh>
   the output tubes

Author:

 Ryan Cabeen

CurvesVertices

Name:

 CurvesVertices

Description:

 Extract all curve vertices

Required Input Arguments:

 --input <Curves>
   input curves

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

CurvesVoxelize

Name:

 CurvesVoxelize

Description:

 Compute a mask by voxelizing curves.  This works by find the voxels that
 intersect the curves and marking them as one.

Required Input Arguments:

 --input <Curves>
   input curves

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

FileFormatUtil

Usage: qit volume [opts] [input_fn(s)]

 a catch-all converter for exchanging data between packages

Options:

 -h, --help      show this help message and exit
 --dtitk         convert dti results to the dti-tk format
 --line-fsl      convert a line image to the FSL format
 --xfib-fsl      convert lines in an fibers directory
 --xfm-fsl       convert an xfm from the FSL format
 --set-forms     set the nifti forms
 --voxel-table   set the nifti forms
 --bvecs-camino  convert camino bvecs
 --bvecs-fsl     convert fsl bvecs

FreesurferImport

Usage: qit FreesurferImport [opts]

convert freesurfer data to nifti and vtk formats with LPI<->RAS coords

Options:

 -h, --help       show this help message and exit
 --input=<dir>    specify the input directory
 --output=<dir>   specify the output directory
 --segmentations  import volumetric segmentations
 --subfields      import volumetric subfield segmentations
 --surfaces       import surfaces
 --resample       resample surface data for group analysis
 --level=<val>    level of detail for spherical surface resampling

FreesurferRegister

Usage: qit FreesurferRegister [opts]

register freesurfer data to diffusion space

Options:

 -h, --help       show this help message and exit
 --input=<dir>    the imported freesurfer dir
 --target=<fn>    the target volume
 --output=<dir>   the output directory
 --interp=<name>  the interpolation method
 --cost=<name>    the registration metric (see flirt)
 --dof=<name>     the transform degrees of freedom (see flirt)
 --bins=<num>     the number of bins (see flirt)

GradientsCat

Name:

 GradientsCat

Description:

 Concatenate two sets of gradients into one

Required Input Arguments:

 --input <Gradients>
   input gradients
 --cat <Gradients>
   gradients to concatenate

Required Output Arguments:

 --output <Gradients>
   output concatenated gradients

Author:

 Ryan Cabeen

GradientsConvert

Name:

 GradientsConvert

Description:

 Convert gradients between file formats

Required Input Arguments:

 --input <Gradients>
   the input gradients

Required Output Arguments:

 --output <Gradients>
   the output gradients

Author:

 Ryan Cabeen

GradientsCreate

Name:

 GradientsCreate

Description:

 Create a gradients file from separate bvecs and bvals

Required Input Arguments:

 --bvecs <Vects>
   the input bvecs
 --bvals <Vects>
   the input bvals

Required Output Arguments:

 --output <Gradients>
   the output gradients

Author:

 Ryan Cabeen

GradientsReduce

Name:

 GradientsReduce

Description:

 Reduce a set of gradients to a which based on user specification

Required Input Arguments:

 --input <Gradients>
   the input gradients

Optional Parameter Arguments:

 --which <String>
   include only specific gradients (comma separated zero-based indices)
 --exclude <String>
   exclude specific gradients (comma separated zero-based indices)
 --shells <String>
   include only specific shells

Required Output Arguments:

 --output <Gradients>
   the output gradients

Author:

 Ryan Cabeen

GradientsTransform

Name:

 GradientsTransform

Description:

 Transform gradient directions

Required Input Arguments:

 --input <Gradients>
   input gradients

Optional Input Arguments:

 --affine <Affine>
   apply an affine transform to gradient directions (and normalize afterwards)

Optional Parameter Arguments:

 --subset <String>
   select a subset of gradients
 --flip <String>
   flip a coodinate (x, y, or z)
 --swap <String>
   swap a pair of coordinates (xy, xz, or yz)
 --perm <String>
   permute by coordinate index, e.g. 1,0,2

Required Output Arguments:

 --output <Gradients>
   output transformed gradients

Author:

 Ryan Cabeen

GradientsTransform$1

 No module named GradientsTransform$1 was found!
 Maybe you are looking for one of these?
   GradientsTransform
   VectsTransform
   CurvesTransform
   GradientTensorSample
   GradientsConvert
   MaskTransform
   VolumeTransform
   GradientsCreate
   MeshTransform
   GradientsCat

MapCat

Name:

 MapCat

Description:

 concatenate map files into a table

Required Parameter Arguments:

 --pattern <Pattern>
   specify an input pattern (substitution like ${name})
 --vars name=value(s)
   specify a list of identifiers

Optional Parameter Arguments:

 --tuples
   expand multiple vars to tuples (default: cartesian product)
 --rows
   expand each input file to a row
 --input-name <String>
   specify the input map name field (Default: name)
 --input-value <String>
   specify the input map value field (Default: value)
 --output-name <String>
   specify the output name field (Default: name)
 --output-value <String>
   specify the output value field (Default: value)
 --na <String>
   specify value for missing entries (Default: NA)
 --skip
   skip missing files
 --include name(s)
   specify which names to include
 --exclude name(s)
   specify which names to exclude

Required Output Arguments:

 --output <File>
   specify the output

Author:

 Ryan Cabeen

MapCatNarrow

Name:

 MapCatNarrow

Description:

 concatenate map files into columns of a table (more efficient than MapCat)

Required Parameter Arguments:

 --pattern <Pattern>
   specify an input pattern (substitution like ${name})
 --vars name=value(s)
   specify a list of identifiers

Optional Parameter Arguments:

 --tuples
   expand multiple vars to tuples (default: cartesian product)
 --input-name <String>
   specify the input map name field (Default: name)
 --input-value <String>
   specify the input map value field (Default: value)
 --output-name <String>
   specify the output map name field (Default: name)
 --output-value <String>
   specify the output map value field (Default: value)
 --na <String>
   specify value for missing entries (Default: NA)
 --skip
   skip missing files
 --include name(s)
   specify which names to include
 --exclude name(s)
   specify which names to exclude

Required Output Arguments:

 --output <File>
   specify the output

Author:

 Ryan Cabeen

MapCatWide

Name:

 MapCatWide

Description:

 concatenate map files into rows of a table (more efficient than MapCat)

Required Parameter Arguments:

 --pattern <Pattern>
   specify an input pattern (substitution like ${name})
 --vars name=value(s)
   specify a list of identifiers

Optional Parameter Arguments:

 --tuples
   expand multiple vars to tuples (default: cartesian product)
 --input-name <String>
   specify the input map name field (Default: name)
 --input-value <String>
   specify the input map value field (Default: value)
 --na <String>
   specify value for missing entries (Default: NA)
 --skip
   skip missing files
 --include name(s)
   specify which names to include
 --exclude name(s)
   specify which names to exclude

Required Output Arguments:

 --output <File>
   specify the output

Author:

 Ryan Cabeen

MapFilter

Name:

 MapFilter

Description:

 filter map files into a single map

Required Input Arguments:

 --pattern <Pattern>
   specify an input pattern (containing a single %)
 --vars value(s)
   specify a list of identifiers (space separated)

Optional Parameter Arguments:

 --name <String>
   specify the entry to select in each map (Default: name)
 --skip
   skip missing or erroneous files

Required Output Arguments:

 --output <File>
   specify the output

Author:

 Ryan Cabeen

MaskBinarize

Name:

 MaskBinarize

Description:

 Binarize a mask to convert all labels to zero or one.

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskBoundary

Name:

 MaskBoundary

Description:

 Close a mask using morphological operations

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --element <String>
   specify an element (Default: cross)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskBox

Name:

 MaskBox

Description:

 Compute the bounding box of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --foreground
   compute box around foreground
 --buffer <Double>
   a buffer in mm

Required Output Arguments:

 --output <Solids>
   output bounding box

Author:

 Ryan Cabeen

MaskBoxCreate

Name:

 MaskBoxCreate

Description:

 Create a mask from a box

Required Input Arguments:

 --input <Solids>
   the input box

Optional Parameter Arguments:

 --delta <double>
   voxel spacing (Default: 1.0)
 --round
   round the starting point

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskClean

Name:

 MaskClean

Description:

 Clean a mask by performing morphological opening followed by closing

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --num <int>
   the number of iterations (Default: 1)
 --largest
   select the largest component as an intermediate step
 --element <String>
   specify an element: cross, cube, or sphere. you can also specify an
   optional size, e.g. cross(3) (Default: cross)
 --outside
   treat voxels outside mask as background

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskClose

Name:

 MaskClose

Description:

 Close a mask morphologically.  This dilates and then erodes the mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --num <int>
   the number of times to erode and dilate the mask (Default: 1)
 --largest
   select the largest component as an intermediate step between erosion and
   dilation
 --element <String>
   specify an element: cross, cube, or sphere. you can also specify an
   optional size, e.g. cross(3) (Default: cross)
 --outside
   treat voxels outside mask as background

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskComponents

Name:

 MaskComponents

Description:

 Compute connected components of a mask.  The output will be sorted by the
 number of voxels per component, e.g. the largest component will have label 1,
 and the second largest will have label 2, etc.

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --full
   use a full 27-voxel neighborhood (default is 6-voxel)
 --which <String>
   include only specific component labels, e.g. "1,2" would select the two
   largest components
 --size <Integer>
   filter out components that are smaller than or equal to the given
   threshold.  e.g. this can be used to filter outliers

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskConvert

Name:

 MaskConvert

Description:

 Convert a mask between file formats

Required Input Arguments:

 --input <Mask>
   input

Required Output Arguments:

 --output <Mask>
   output

Author:

 Ryan Cabeen

MaskCreate

Name:

 MaskCreate

Description:

 Create a mask based on user specified parameters

Optional Parameter Arguments:

 --deltax <double>
   voxel spacing in x (Default: 1.0)
 --deltay <double>
   voxel spacing in y (Default: 1.0)
 --deltaz <double>
   voxel spacing in z (Default: 1.0)
 --numx <int>
   number of voxels in x (Default: 128)
 --numy <int>
   number of voxels in y (Default: 128)
 --numz <int>
   number of voxels in z (Default: 1)
 --startx <double>
   starting position in x (Default: 0.0)
 --starty <double>
   starting position in y (Default: 0.0)
 --startz <double>
   starting position in z (Default: 0.0)
 --label <int>
   constant label (Default: 0)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskCrop

Name:

 MaskCrop

Description:

 Crop a mask down to a smaller mask (only one criteria per run)

Required Input Arguments:

 --input <Mask>
   input mask

Optional Input Arguments:

 --mask <Mask>
   a mask
 --solids <Solids>
   some soids

Optional Parameter Arguments:

 --range <String>
   a range specification, e.g. start:end,start:end,start:end
 --invert
   invert the selection
 --pad <int>
   a padding size in voxels (Default: 0)

Required Output Arguments:

 --output <Mask>
   the output mask

Author:

 Ryan Cabeen

MaskDilate

Name:

 MaskDilate

Description:

 Dilate a mask morphologically.

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --num <int>
   the number of times to dilate the mask (Default: 1)
 --element <String>
   specify an element: cross, cube, or sphere. you can also specify an
   optional size, e.g. cross(3) (Default: cross)
 --outside
   treat voxels outside mask as background

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskDistanceTransform

Name:

 MaskDistanceTransform

Description:

 Compute a distance transform using pff's fast algorithm

Required Input Arguments:

 --input <Mask>
   the input mask

Optional Parameter Arguments:

 --signed
   compute a signed transform

Required Output Arguments:

 --output <Volume>
   the output distance transform

Author:

 Ryan Cabeen

Citation:

 Felzenszwalb, P., & Huttenlocher, D. (2004). Distance transforms of sampled
 functions. Cornell University.

MaskEdge

Name:

 MaskEdge

Description:

 Detect the edges of a input mask

Required Input Arguments:

 --input <Mask>
   input input

Optional Parameter Arguments:

 --binary
   binarize the edges
 --full
   use a full neighborhood

Required Output Arguments:

 --output <Mask>
   output input

Author:

 Ryan Cabeen

MaskErode

Name:

 MaskErode

Description:

 Erode a mask morphologically

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --num <int>
   the number of iterations (Default: 1)
 --outside
   treat voxels outside mask as background
 --verbose
   print messages

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskExtract

Name:

 MaskExtract

Description:

 Extract specific labels from a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Input Arguments:

--lookup
input lookup table (must store the index and name of each label) Optional Parameter Arguments: --label <String> the label(s) to extract (comma delimited, e.g. 1,2,3 or lh-temporal,rh-temporal if a lookup is used) (Default: 1) --mode <MaskExtractMode> the mode for extracting labels (Options: Binary, Preserve, Distinct) (Default: Binary) --name <String> the name field in the lookup table (Default: name) --index <String> the index field in the lookup table (Default: index) Required Output Arguments: --output <Mask> output mask Author: Ryan Cabeen

MaskFill

Name:

 MaskFill

Description:

 Close a mask morphologically

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskFuse

Name:

 MaskFuse

Description:

 fuse volumes

Required Input Arguments:

 --input <Mask(s)>
   the input volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Optional Parameter Arguments:

 --pattern <String(s)>
   specify a list of names that will be substituted with input %s

Optional Output Arguments:

 --output-label <Mask>
   specify the output maxima likelihood label
 --output-prob <Volume>
   specify the output label probability

Author:

 Ryan Cabeen

MaskGreater

Name:

 MaskGreater

Description:

 Extract the larger components of a mesh

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --minimum <double>
   the minima volume (Default: 25.0)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskHull

Name:

 MaskHull

Description:

 Compute the convex hull of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

Citation:

 Barber, C. B., Dobkin, D. P., & Huhdanpaa, H. (1996). The quickhull algorithm
 for convex hulls. ACM Transactions on Mathematical Software (TOMS), 22(4),
 469-483.

MaskIntersection

Name:

 MaskIntersection

Description:

 Compute the logical AND of two masks

Required Input Arguments:

 --left <Mask>
   input left mask
 --right <Mask>
   input right mask

Optional Parameter Arguments:

 --mode <MaskIntersectionMode>
   specify what label should be returned (Options: Left, Right, Max, Min, Sum,
   Product, One) (Default: Left)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskInvert

Name:

 MaskInvert

Description:

 Invert the labels of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskLargest

Name:

 MaskLargest

Description:

 Extract the largest component of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskLesser

Name:

 MaskLesser

Description:

 Extract the smaller components of a mesh

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --maximum <double>
   the maxima volume (Default: 25.0)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskList

Name:

 MaskList

Description:

 Create a list of regions from a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --zero
   include zero
 --base <String>
   specify a basename (Default: region)
 --name <String>
   specify the lookup name field (Default: name)
 --index <String>
   specify the output index name (Default: index)

Required Output Arguments:

--output
output table Author: Ryan Cabeen

MaskMarchingCubes

Name:

 MaskMarchingCubes

Description:

 Extract surfaces from a mask.  If there are multiple labels in the volume,
 distinct meshes will be produced for each label.

Required Input Arguments:

 --input <Mask>
   input mask

Optional Input Arguments:

--table
a table listing a subset of indices Optional Parameter Arguments: --std <Double> perform Gaussian smoothing before surface extraction --support <Integer> use a given support in voxels for smoothing (Default: 3) --level <Double> use a given isolevel for smoothed surface extraction (Default: 0.5) --which <String> a string specifying a subset of labels, e.g. 1,2,4:6 --tindex <String> the index field name to use in the table (Default: index) --mindex <String> the mesh attribute for the index value (default is "label") (Default: label) Required Output Arguments: --output <Mesh> output mesh Author: Ryan Cabeen Citation: Lorensen, W. E., & Cline, H. E. (1987, August). Marching cubes: A high resolution 3D surface construction algorithm. In ACM siggraph computer graphics (Vol. 21, No. 4, pp. 163-169). ACM.

MaskMarchingSquares

Name:

 MaskMarchingSquares

Description:

 Extract contours from slices of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --dim <String>
   volume channel to contour (x, y, or z) (Default: z)
 --start <int>
   starting slice index (Default: 0)
 --step <int>
   number of slices between contours (Default: 1)

Required Output Arguments:

 --output <Curves>
   output curves

Author:

 Ryan Cabeen

Citation:

 Maple, C. (2003, July). Geometric design and space planning using the
 marching squares and marching cube algorithms. In Geometric Modeling and
 Graphics, 2003. Proceedings. 2003 International Conference on (pp. 90-95).
 IEEE.

MaskMeasure

Name:

 MaskMeasure

Description:

 Measure properties of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Input Arguments:

--lookup
use a lookup for region names Optional Parameter Arguments: --nameField <String> specify the lookup name field (Default: name) --indexField <String> specify the output index field name (Default: index) --countField <String> specify the voxel count field name (Default: count) --volumeField <String> specify the voxel count field name (Default: volume) --xField <String> the region centroid x field (Default: meanx) --yField <String> the region centroid y field (Default: meany) --zField <String> the region centroid z field (Default: meanz) Required Output Arguments: --output
output table Author: Ryan Cabeen

MaskNodeLink

Name:

 MaskNodeLink

Description:

 Create a node link representation of mask connectivity in a mesh

Required Input Arguments:

 --input <Mask>
   input mask
--lookup
input table --attributes
input attributes Optional Parameter Arguments: --index <String> index (Default: index) --name <String> name (Default: name) --group <String> group (Default: group) --value <String> value (Default: value) --radius <double> radius (Default: 10.0) --subdiv <int> subdiv (Default: 2) Optional Output Arguments: --links <Curves> output links --nodes <Mesh> output nodes Author: Ryan Cabeen

MaskOpen

Name:

 MaskOpen

Description:

 Open a mask using morphological operations.  This first erodes the mask and
 then dilates it.

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --num <int>
   the number of times to erode and dilate the mask (Default: 1)
 --largest
   select the largest component as an intermediate step between erosion and
   dilation
 --element <String>
   specify an element: cross, cube, or sphere. you can also specify an
   optional size, e.g. cross(3) (Default: cross)
 --outside
   treat voxels outside mask as background

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskOrigin

Name:

 MaskOrigin

Description:

 Set the origin of a mask

Required Input Arguments:

 --input <Mask>
   the input Mask

Optional Parameter Arguments:

 --x <double>
   the origin in x (Default: 0.0)
 --y <double>
   the origin in y (Default: 0.0)
 --z <double>
   the origin in z (Default: 0.0)

Required Output Arguments:

 --output <Mask>
   the output Mask

Author:

 Ryan Cabeen

MaskPhantomNoisy

Name:

 MaskPhantomNoisy

Description:

 Generate a noisy mask

Optional Parameter Arguments:

 --width <int>
   image width (Default: 100)
 --height <int>
   image height (Default: 100)
 --slices <int>
   image slices (Default: 1)
 --labels <int>
   the number of labels to use (Default: 1)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskPrintInfo

Name:

 MaskPrintInfo

Description:

 Print basic information about a mask

Required Input Arguments:

 --input <Mask>
   the input mask

Optional Parameter Arguments:

 --stats
   print statistics

Author:

 Ryan Cabeen

MaskPrototype

Name:

 MaskPrototype

Description:

 Create a mask from example data

Optional Input Arguments:

 --mask <Mask>
   an example mask
 --volume <Volume>
   an example volume

Optional Parameter Arguments:

 --label <int>
   the default label (Default: 0)

Required Output Arguments:

 --output <Mask>
   output

Author:

 Ryan Cabeen

MaskRegionMerge

Name:

 MaskRegionMerge

Description:

 Merge small regions using an adjacency graph

Required Input Arguments:

 --input <Mask>
   input region input

Optional Parameter Arguments:

 --threshold <double>
   the input threshold (Default: 10.0)
 --full
   use a full 27-voxel neighborhood (default is 6-voxel)

Required Output Arguments:

 --output <Mask>
   output input

Author:

 Ryan Cabeen

MaskRegionsExtract

Name:

 MaskRegionsExtract

Description:

 extract mesh models from a mask for each region

Required Input Arguments:

 --regions <Mask>
   specify input region of interest(s)
--lookup
a table listing the names of regions Optional Input Arguments: --mask <Mask> specify a mask for including voxels Optional Parameter Arguments: --name <String> specify a lookup table field for region names (Default: name) --index <String> specify a lookup table field for region index (label) (Default: index) --include name(s) specify which names to include --exclude name(s) specify which names to exclude --support <Integer> specify a filter support size (Default: 3) --std <Double> specify a smoothing bandwidth --level <Double> specify a isolevel (Default: 0.5) Optional Output Arguments: --output-mesh <Pattern> specify an output pattern (contains %s) for mesh output --output-mask <Pattern> specify an output pattern (contains %s) for mask output Author: Ryan Cabeen

MaskRegionsMeasure

Name:

 MaskRegionsMeasure

Description:

 measure statistics of volume data in a set of regions of interest

Required Input Arguments:

 --regions <Mask>
   specify input region of interest(s)
--lookup
a table listing the names of regions Optional Input Arguments: --mask <Mask> specify a mask for including voxels Optional Parameter Arguments: --volume <String=Volume> [...] specify volumes to measure --name <String> specify a lookup table field for region names (Default: name) --index <String> specify a lookup table field for region index (label) (Default: index) --na <String> specify a name for missing values (Default: NA) Required Output Arguments: --output <Directory> specify an output directory Author: Ryan Cabeen

MaskRelabel

Name:

 MaskRelabel

Description:

 Relabel a mask by replacing voxel labels with new values

Required Input Arguments:

 --mask <Mask>
   input mask
--mapping
input mapping (includes fields named 'from' and 'to') Optional Input Arguments: --lookup
input lookup Optional Parameter Arguments: --preserve preserve the input labels if possible --names use names for remapping (instead of index labels) --from <String> specify a from field to us in mapping (Default: from) --to <String> specify a to field to us in mapping (Default: to) --name <String> the name field (Default: name) --index <String> the index field (Default: index) Required Output Arguments: --outputMask <Mask> output mask Optional Output Arguments: --outputLookup
output lookup Author: Ryan Cabeen

MaskResample

Name:

 MaskResample

Description:

 Resample a mask with a different voxel size

Required Input Arguments:

 --input <Mask>
   the input volume

Optional Parameter Arguments:

 --dx <double>
   the voxel size in x (Default: 1.0)
 --dy <double>
   the voxel size in y (Default: 1.0)
 --dz <double>
   the voxel size in z (Default: 1.0)

Required Output Arguments:

 --output <Mask>
   the output volume

Author:

 Ryan Cabeen

MaskRestoreMRF

Name:

 MaskRestoreMRF

Description:

 Restore a mask using a markov random field with loopy belief propagation

Required Input Arguments:

 --input <Mask>
   input mask

Optional Input Arguments:

 --mask <Mask>
   a mask of the area to restore

Optional Parameter Arguments:

 --cost <double>
   the cost for changing a voxel label (Default: 0.75)
 --data <double>
   the weight for the data term (Default: 1.0)
 --smooth <double>
   the weight for the smoothness term (Default: 1.0)
 --iters <int>
   the number of belief propagation iterations (Default: 50)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

Citation:

 Felzenszwalb, P. F., & Huttenlocher, D. P. (2006). Efficient belief
 propagation for early vision. International journal of computer vision,
 70(1), 41-54.

MaskSampleVects

Name:

 MaskSampleVects

Description:

 Sample vects from a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --count <int>
   the number of samples per voxel (Default: 1)
 --limit <int>
   the label to extract (Default: 10000)

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

MaskSet

Name:

 MaskSet

Description:

 Set the values of a mask

Required Input Arguments:

 --input <Mask>
   the input mask

Optional Input Arguments:

 --solids <Solids>
   some solids
 --vects <Vects>
   some vects
 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --clear
   clear the input labels before setting anything
 --range <String>
   a range, e.g. start:end,start:end,start:end
 --label <int>
   the label to set (Default: 1)

Required Output Arguments:

 --output <Mask>
   the output mask

Author:

 Ryan Cabeen

MaskSetTable

Name:

 MaskSetTable

Description:

 Create a table listing regions of a mask

Required Input Arguments:

 --reference <Mask>
   input reference
--table
input table Optional Input Arguments: --lookup
a lookup table to relate names to indices Optional Parameter Arguments: --merge <String> a field name to merge on (Default: name) --index <String> the index field name (Default: index) --value <String> a field to set (Default: value) --background <double> a background value (Default: 0.0) --missing <Double> an missing value Required Output Arguments: --output <Volume> output volume Author: Ryan Cabeen

MaskShell

Name:

 MaskShell

Description:

 Compute the shell of a mask (the voxels at the boundary of the mesh)

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --outer
   create a shell outside the mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskSkeleton

Name:

 MaskSkeleton

Description:

 Skeletonize a mask using medial axis thinning.  Based on Hanno Homan's
 implementation of Lee et al. at http://hdl.handle.net/1926/1292

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

Citation:

 Lee, Ta-Chih, Rangasami L. Kashyap, and Chong-Nam Chu. Building skeleton
 models via 3-D medial surface axis thinning algorithms. CVGIP: Graphical
 Models and Image Processing 56.6 (1994): 462-478.

MaskSort

Name:

 MaskSort

Description:

 Sort the labels of a mask by their size

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskStandardize

Name:

 MaskStandardize

Description:

 Standardize the pose of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Output Arguments:

 --output <Mask>
   output mask
 --xfm <Affine>
   output affine
 --invxfm <Affine>
   output inverse affine

Author:

 Ryan Cabeen

MaskTable

Name:

 MaskTable

Description:

 Create a table listing regions of a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --nameField <String>
   the region name field (Default: name)
 --indexField <String>
   the region label field (Default: index)
 --namePattern <String>
   a pattern for naming regions (Default: region%d)
 --xField <String>
   the region centroid x field (Default: x)
 --yField <String>
   the region centroid y field (Default: y)
 --zField <String>
   the region centroid z field (Default: z)
 --name
   include a name field
 --centroid
   include a centroid fields

Required Output Arguments:

--output
output table Author: Ryan Cabeen

MaskTransform

Name:

 MaskTransform

Description:

 Transform a mask

Required Input Arguments:

 --input <Mask>
   input volume

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)
 --mask <Mask>
   input mask
 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --background <Integer>
   a label for filling background voxels

Required Output Arguments:

 --output <Mask>
   output volume

Author:

 Ryan Cabeen

MaskUnion

Name:

 MaskUnion

Description:

 Combine two masks into one.  By default, the mask labels are preserved, but
 the relabel flag will use new and distinct labels.

Required Input Arguments:

 --left <Mask>
   input left mask
 --right <Mask>
   input right mask

Optional Parameter Arguments:

 --relabel
   combine the masks using distinct values
 --max
   use the maximum label when masks overlap (default is to use the right)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MaskVects

Name:

 MaskVects

Description:

 Extract a vector for each foreground voxel

Required Input Arguments:

 --input <Mask>
   input mask

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

MaskZoom

Name:

 MaskZoom

Description:

 Zoom a mask

Required Input Arguments:

 --input <Mask>
   input mask

Optional Parameter Arguments:

 --factor <Double>
   an isotropic scaling factor (Default: 2.0)
 --isotropic <Double>
   an isotropic scaling factor
 --fi <Double>
   a scaling factor in i
 --fj <Double>
   a scaling factor in j
 --fk <Double>
   a scaling factor in k

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

MatrixConvert

Name:

 MatrixConvert

Description:

 Convert a matrix between file formats

Required Input Arguments:

 --input <Matrix>
   input matrix

Required Output Arguments:

 --output <Matrix>
   output matrix

Author:

 Ryan Cabeen

MatrixCreate

Name:

 MatrixCreate

Description:

 Create a matrix

Required Parameter Arguments:

 --identity <Integer>
   create an identity matrix with the given channel

Required Output Arguments:

 --output <Matrix>
   output matrix

Author:

 Ryan Cabeen

MatrixInvert

Name:

 MatrixInvert

Description:

 Invert a matrix

Required Input Arguments:

 --input <Matrix>
   input matrix

Required Output Arguments:

 --output <Matrix>
   output matrix

Author:

 Ryan Cabeen

MatrixMeasureBatch

Usage: qit MatrixMeasureBatch [opts]

measure properties of network matrices in batch mode

Options:

 -h, --help          show this help message and exit
 --matrix=<pattern>  the filename pattern (%s is substituted)
 --nodes=<list>      a list of node names
 --names=<list>      a list of names to process in batch
 --output=<dir>      the output directory

MatrixOrthogonalize

Name:

 MatrixOrthogonalize

Description:

 Orthogonalize a matrix

Required Input Arguments:

 --input <Matrix>
   input matrix

Required Output Arguments:

 --output <Matrix>
   output matrix

Author:

 Ryan Cabeen

MatrixPrintInfo

Name:

 MatrixPrintInfo

Description:

 Print basic information about a matrix

Required Input Arguments:

 --input <Matrix>
   the input matrix

Author:

 Ryan Cabeen

MatrixTranspose

Name:

 MatrixTranspose

Description:

 Transpose a matrix

Required Input Arguments:

 --input <Matrix>
   input matrix

Required Output Arguments:

 --output <Matrix>
   output matrix

Author:

 Ryan Cabeen

MeshAttributes

Name:

 MeshAttributes

Description:

 Manipulate mesh vertex attributes.  Operations support comma-delimited lists

Required Input Arguments:

 --input <Mesh>
   the input Mesh

Optional Parameter Arguments:

 --copy <String>
   copy attribute (x=y syntax)
 --rename <String>
   rename attribute (x=y syntax)
 --remove <String>
   remove attribute (- for all)
 --retain <String>
   retain the given attributes and remove others)

Required Output Arguments:

 --output <Mesh>
   the output Mesh

Author:

 Ryan Cabeen

MeshBox

Name:

 MeshBox

Description:

 Get the bounding box of a mesh

Required Input Arguments:

 --input <Mesh>
   input mesh

Required Output Arguments:

 --output <Solids>
   output box

Author:

 Ryan Cabeen

MeshCat

Name:

 MeshCat

Description:

 Concatentate two meshes

Required Input Arguments:

 --left <Mesh>
   input left
 --right <Mesh>
   input right

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCatBatch

Name:

 MeshCatBatch

Description:

 Concatenate mesh files

Required Input Arguments:

 --input <File(s)>
   specify an input meshes

Optional Parameter Arguments:

 --names <String(s)>
   use pattern-based input with the given names
 --label
   add a label attribute
 --attr <String>
   use a specific label attribute name (Default: label)

Required Output Arguments:

 --output <File>
   specify the output

Optional Output Arguments:

 --output-table <File>
   specify the output table name

Author:

 Ryan Cabeen

MeshComponents

Name:

 MeshComponents

Description:

 Compute connected components of a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --largest
   retain only the largest component
 --attr <String>
   the name of the component attribute (Default: index)
 --select <String>
   retain components selected with the given attribute
 --area <Double>
   retain components above a given surface area
 --invert
   invert the selection

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshConvert

Name:

 MeshConvert

Description:

 Convert a mesh between file formats

Required Input Arguments:

 --input <Mesh>
   input mesh

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateBox

Name:

 MeshCreateBox

Description:

 Create a box

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateCylinder

Name:

 MeshCreateCylinder

Description:

 Create a cylinder mesh

Optional Parameter Arguments:

 --startx <double>
   input start x coordinate (Default: 0.0)
 --starty <double>
   input start y coordinate (Default: 0.0)
 --startz <double>
   input start z coordinate (Default: 0.0)
 --endx <double>
   input end x coordinate (Default: 1.0)
 --endy <double>
   input end y coordinate (Default: 10.0)
 --endz <double>
   input end z coordinate (Default: 10.0)
 --radius <double>
   input radius (Default: 5.0)
 --resolution <int>
   input resolution (Default: 5)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateHemisphere

Name:

 MeshCreateHemisphere

Description:

 Create a hemisphere mesh

Optional Parameter Arguments:

 --sudiv <int>
   the number of subdivisions (Default: 1)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateIcosahedron

Name:

 MeshCreateIcosahedron

Description:

 Create a icosahedron

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateOctahedron

Name:

 MeshCreateOctahedron

Description:

 Create an octahedron

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateSphere

Name:

 MeshCreateSphere

Description:

 Create a sphere mesh

Optional Parameter Arguments:

 --x <double>
   input x coordinate (Default: 0.0)
 --y <double>
   input y coordinate (Default: 0.0)
 --z <double>
   input z coordinate (Default: 0.0)
 --radius <double>
   input radius (Default: 5.0)
 --subdiv <int>
   input subdivisions (Default: 2)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCreateTetrahedron

Name:

 MeshCreateTetrahedron

Description:

 Create a tetrahedron

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshCrop

Module: MeshCrop Field: selection Message: cannot have datatype 'String'. (hint: switch it to a @ModuleParameter)

Module validation revealed 1 invalid fields. See report results above.

MeshCropSelection

Name:

 MeshCropSelection

Description:

 Crop a mesh from a selection

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --invert
   invert the selection
 --attr <String>
   the selection attribute (Default: selection)

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshExtract

Name:

 MeshExtract

Description:

 Extract a subset of a mesh that matches the given attribute values

Required Input Arguments:

 --input <Mesh>
   input mesh

Optional Parameter Arguments:

 --attr <String>
   the attribute name of the label used to select (Default: label)
 --include <String>
   which labels to include, e.g. 1,2,3:5
 --exclude <String>
   which labels to exclude, e.g. 1,2,3:5

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshFeatures

Name:

 MeshFeatures

Description:

 Compute geometric features of a mesh at each vertex.  A locally quadratic
 approximation at each vertex is used to find curvature features

Required Input Arguments:

 --input <Mesh>
   the input mesh

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshFlipNormals

Name:

 MeshFlipNormals

Description:

 Flip the normals of a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshFuse

Name:

 MeshFuse

Description:

 fuse meshes

Required Input Arguments:

 --input <Meshes>
   the input meshes

Optional Parameter Arguments:

 --pattern <String(s)>
   specify a list of names that will be substituted with input %s

Optional Output Arguments:

 --vector <String>
   specify vector attributes (comma-separated)
 --discrete <String>
   specify discrete attributes (comma-separated)
 --output <Volume>
   specify the output label probability

Author:

 Ryan Cabeen

MeshGetVects

Name:

 MeshGetVects

Description:

 Extract a mesh vertex attribute as vectors

Required Input Arguments:

 --mesh <Mesh>
   input mesh

Optional Parameter Arguments:

 --name <String>
   the destination attribute name (Default: attr)

Required Output Arguments:

 --output <Vects>
   output mesh

Author:

 Ryan Cabeen

MeshHoleFill

Name:

 MeshHoleFill

Description:

 Fill holes in a mesh.  This can be applied to either the entire mesh or a
 selection

Required Input Arguments:

 --input <Mesh>
   the input mesh

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshHull

Name:

 MeshHull

Description:

 Compute the convex hull of a mesh

Required Input Arguments:

 --input <Mesh>
   input mesh

Required Output Arguments:

 --output <Mesh>
   output hull mesh

Author:

 Ryan Cabeen

Citation:

 Barber, C. B., Dobkin, D. P., & Huhdanpaa, H. (1996). The quickhull algorithm
 for convex hulls. ACM Transactions on Mathematical Software (TOMS), 22(4),
 469-483.

MeshMath

Name:

 MeshMath

Description:

 Evaluate an expression at each vertex of a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: x > 0.5)
 --result <String>
   the attribute name for the result (Default: result)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshMeasure

Name:

 MeshMeasure

Description:

 Measure global properties of a mesh

Required Input Arguments:

 --input <Mesh>
   input mesh

Required Output Arguments:

--output
output table Author: Ryan Cabeen

MeshNormals

Name:

 MeshNormals

Description:

 Compute vertex normals of a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshPrintInfo

Name:

 MeshPrintInfo

Description:

 Print basic information about a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --stats
   print statistics
 --area
   print statistics of triangle areas

Author:

 Ryan Cabeen

MeshSample

Name:

 MeshSample

Description:

 Sample a volume at input vertices

Required Input Arguments:

 --input <Mesh>
   input input
 --volume <Volume>
   input volume

Optional Parameter Arguments:

 --interp <InterpolationType>
   interpolation method (Options: Nearest, Trilinear, Tricubic, Gaussian,
   GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)
 --attr <String>
   attribute name (Default: sampled)

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshSelect

Name:

 MeshSelect

Description:

 Select vertices of a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Input Arguments:

 --solids <Solids>
   some solids

Optional Parameter Arguments:

 --boundary
   select the boundary
 --invert
   invert the selection
 --attr <String>
   the selection attribute (Default: selection)
 --value <double>
   the selection value (Default: 1.0)

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshSelectionClose

Name:

 MeshSelectionClose

Description:

 Close a mesh vertex selection

Required Input Arguments:

 --input <Mesh>
   input mesh

Optional Parameter Arguments:

 --largest
   select the largest component as an intermediate step
 --num <int>
   the number of iterations (Default: 1)
 --attr <String>
   the selection attribute (Default: selection)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshSelectionComponents

Name:

 MeshSelectionComponents

Description:

 Compute connected components of a mesh selection

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --largest
   retain only the largest component
 --attr <String>
   the name of the selection attribute (Default: selection)

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshSelectionDilate

Name:

 MeshSelectionDilate

Description:

 Dilate a mesh selection

Required Input Arguments:

 --input <Mesh>
   input mesh

Optional Parameter Arguments:

 --num <int>
   the number of iterations (Default: 1)
 --attr <String>
   the selection attribute (Default: selection)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshSelectionErode

Name:

 MeshSelectionErode

Description:

 Erode a mesh selection

Required Input Arguments:

 --input <Mesh>
   input mesh

Optional Parameter Arguments:

 --num <int>
   the number of iterations (Default: 1)
 --attr <String>
   the selection attribute (Default: selection)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshSelectionOpen

Name:

 MeshSelectionOpen

Description:

 Open a mesh selection

Required Input Arguments:

 --input <Mesh>
   input mesh

Optional Parameter Arguments:

 --largest
   select the largest component as an intermediate step
 --num <int>
   the number of iterations (Default: 1)
 --attr <String>
   the selection attribute (Default: selection)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshSetTable

Name:

 MeshSetTable

Description:

 Create a table listing regions of a mask

Required Input Arguments:

 --mesh <Mesh>
   input mesh
--table
input table Optional Input Arguments: --lookup
a lookup table to relate names to indices Optional Parameter Arguments: --merge <String> a field name to merge on (Default: name) --index <String> the table index field name (Default: index) --value <String> a table field to get (can be comma delimited) (Default: value) --mindex <String> the mesh index field name (defaults to table index field name) --mvalue <String> the mesh value field name (defaults to table value field name) --background <double> a background value (Default: 0.0) --missing <Double> an missing value Required Output Arguments: --output <Mesh> output mesh Author: Ryan Cabeen

MeshSetVects

Name:

 MeshSetVects

Description:

 Add vects as an attribute on a mesh (number of vects must match the number of
 vertices)

Required Input Arguments:

 --mesh <Mesh>
   input mesh
 --vects <Vects>
   input vects

Optional Parameter Arguments:

 --name <String>
   the destination attribute name (Default: attr)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshSimplify

Name:

 MeshSimplify

Description:

 Simplify a input by removing short edges

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --maxiter <Integer>
   maxima number of iterations (Default: 10000)
 --maxvert <Integer>
   maxima number of vertices
 --maxedge <Integer>
   maxima number of edges
 --maxface <Integer>
   maxima number of faces
 --meanarea <Double>
   maxima average face surface area

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshSmooth

Name:

 MeshSmooth

Description:

 Smooth a mesh

Required Input Arguments:

 --input <Mesh>
   the input

Optional Parameter Arguments:

 --num <int>
   a number of iterations (Default: 5)
 --lambda <Double>
   the lambda laplacian smoothing parameter (Default: 0.3)
 --mu <Double>
   the optional mu parameter for Taubin's method

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

Citation:

 Taubin, G. (1995, September). A signal processing approach to fair surface
 design. In Proceedings of the 22nd annual conference on Computer graphics and
 interactive techniques (pp. 351-358). ACM.

MeshSubdivide

Name:

 MeshSubdivide

Description:

 Subdivide a mesh.  Each triangle is split into four with new vertices that
 split each edge in two.

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --num <int>
   a number of subdivisions (Default: 1)

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshTable

Name:

 MeshTable

Description:

 Create a table from mesh vertex attributes

Required Input Arguments:

 --input <Mesh>
   input input

Optional Parameter Arguments:

 --which <String>
   which attributes to retain (comma separated) (Default: x,y,z)

Required Output Arguments:

--output
output table Author: Ryan Cabeen

MeshTransform

Name:

 MeshTransform

Description:

 Transform a mesh

Required Input Arguments:

 --input <Mesh>
   input mesh

Optional Input Arguments:

 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

MeshVertexMath

Name:

 MeshVertexMath

Description:

 Evaluate an expression at each vertex of a mesh

Required Input Arguments:

 --input <Mesh>
   the input mesh

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: x > 0.5)
 --result <String>
   the attribute for the result (Default: result)

Required Output Arguments:

 --output <Mesh>
   the output mesh

Author:

 Ryan Cabeen

MeshVertices

Name:

 MeshVertices

Description:

 Extract the vertices of a mesh

Required Input Arguments:

 --input <Mesh>
   input mesh

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

MeshView$32$1

 No module named MeshView$32$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$33$1

 No module named MeshView$33$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$34$1

 No module named MeshView$34$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$35$1

 No module named MeshView$35$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$36$1

 No module named MeshView$36$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$37$1

 No module named MeshView$37$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$38$1

 No module named MeshView$38$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$39$1

 No module named MeshView$39$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshView$40$1

 No module named MeshView$40$1 was found!
 Maybe you are looking for one of these?
   MeshVertices
   MeshSimplify
   MeshSetTable
   MeshMeasure
   MeshSelect
   MeshFeatures
   MeshCreateBox
   MeshVoxelize
   MeshSetVects
   MeshGetVects

MeshVoxelize

Name:

 MeshVoxelize

Description:

 Voxelize a mesh to a mask (should be watertight if the mesh is also)

Required Input Arguments:

 --input <Mesh>
   input input
 --reference <Mask>
   reference mask

Optional Parameter Arguments:

 --label <Integer>
   a label to draw (Default: 1)
 --fill
   fill the inside of the mask

Required Output Arguments:

 --output <Mask>
   the output mask

Author:

 Ryan Cabeen

ParticleCurvesCoder$1

 No module named ParticleCurvesCoder$1 was found!
 Maybe you are looking for one of these?
   CurvesConvert
   CurvesCompare
   CurvesCrop
   TableConvert
   CurvesSelect
   CurvesVoxelize
   CurvesReduce
   CurvesCull
   CurvesOrient
   CurvesCat

ParticleMeshCoder$1

 No module named ParticleMeshCoder$1 was found!
 Maybe you are looking for one of these?
   MeshConvert
   TableConvert
   TableMerge
   MeshFlipFaces
   CurvesConvert
   GradientsConvert
   MeshCrop
   AffineConvert
   TableMath
   MaskRestoreMRF

RenderVolumeRaycastCPU$24

 No module named RenderVolumeRaycastCPU$24 was found!
 Maybe you are looking for one of these?
   VolumePoseCopy
   VolumeJacobian
   VolumeMaxProb
   VolumeSurfacePlot
   VolumeResample
   VolumeReslice
   VolumeSpharmPeaks
   VolumeDwiBaseline
   VolumeCat
   VolumeMarchingCubes

SolidsBox

Name:

 SolidsBox

Description:

 Compute the bounding box of solids

Required Input Arguments:

 --input <Solids>
   input solids

Required Output Arguments:

 --output <Solids>
   output bounding box

Author:

 Ryan Cabeen

SolidsCat

Name:

 SolidsCat

Description:

 Concatenate solids

Required Input Arguments:

 --left <Solids>
   input solids
 --right <Solids>
   input solids

Required Output Arguments:

 --output <Solids>
   output solids

Author:

 Ryan Cabeen

SolidsConvert

Name:

 SolidsConvert

Description:

 Convert solids between file formats

Required Input Arguments:

 --input <Solids>
   input solids

Required Output Arguments:

 --output <Solids>
   output sphere

Author:

 Ryan Cabeen

SolidsCreateBox

Name:

 SolidsCreateBox

Description:

 Create a soilds object containing a box

Optional Parameter Arguments:

 --xmin <double>
   a box minima value in x (Default: 0.0)
 --ymin <double>
   a box minima in y (Default: 0.0)
 --zmin <double>
   a box minima in z (Default: 0.0)
 --xmax <double>
   a box maxima value in x (Default: 1.0)
 --ymax <double>
   a box maxima in y (Default: 1.0)
 --zmax <double>
   a box maxima in z (Default: 1.0)

Required Output Arguments:

 --output <Solids>
   output solids

Author:

 Ryan Cabeen

SolidsCreateEmpty

Name:

 SolidsCreateEmpty

Description:

 Create an empty soilds object

Required Output Arguments:

 --output <Solids>
   output solids

Author:

 Ryan Cabeen

SolidsCreatePlane

Name:

 SolidsCreatePlane

Description:

 Create a soilds object containing a plane

Optional Parameter Arguments:

 --xpoint <double>
   the x coordinate of a point on the plane (Default: 0.0)
 --ypoint <double>
   the y coordinate of a point on the plane (Default: 0.0)
 --zpoint <double>
   the z coordinate of a point on the plane (Default: 0.0)
 --xnormal <double>
   the x coordinate of the plane normal (Default: 0.0)
 --ynormal <double>
   the y coordinate of the plane normal (Default: 0.0)
 --znormal <double>
   the z coordinate of the plane normal (Default: 0.0)

Required Output Arguments:

 --output <Solids>
   output solids

Author:

 Ryan Cabeen

SolidsCreateSphere

Name:

 SolidsCreateSphere

Description:

 Create a soilds object containing a sphere

Optional Parameter Arguments:

 --x <double>
   a sphere x center (Default: 0.0)
 --y <double>
   a sphere y center (Default: 0.0)
 --z <double>
   a sphere z center (Default: 0.0)
 --radius <double>
   a sphere radius (Default: 10.0)

Required Output Arguments:

 --output <Solids>
   output solids

Author:

 Ryan Cabeen

SolidsMask

Name:

 SolidsMask

Description:

 Create a mask from solids

Required Input Arguments:

 --input <Solids>
   input solids

Optional Parameter Arguments:

 --dx <double>
   sample spacing in x (Default: 1.0)
 --dy <double>
   sample spacing in x (Default: 1.0)
 --dz <double>
   sample spacing in x (Default: 1.0)
 --label <int>
   label (Default: 1)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

SolidsPrintInfo

Name:

 SolidsPrintInfo

Description:

 Print basic information about a solids

Required Input Arguments:

 --input <Solids>
   the input solids

Author:

 Ryan Cabeen

SolidsSample

Name:

 SolidsSample

Description:

 Sample vects inside solids

Required Input Arguments:

 --input <Solids>
   input solids

Optional Parameter Arguments:

 --num <int>
   the number of points to sample (Default: 100)

Required Output Arguments:

 --output <Vects>
   output sampled vects

Author:

 Ryan Cabeen

SolidsToWaypoints

Name:

 SolidsToWaypoints

Description:

 Create a waypoint mask from two solids

Required Input Arguments:

 --a <Solids>
   first input set of solids
 --b <Solids>
   second input set of solids
 --ref <Mask>
   input reference mask

Required Output Arguments:

 --output <Mask>
   output waypoint mask

Author:

 Ryan Cabeen

SurfaceMeasure

Name:

 SurfaceMeasure

Description:

 Compute measures of brain surfaces, including surface area, hull surface
 area, gyrification, and lateralization, i.e. (left - right) / (left + right).

Required Input Arguments:

 --input <dir>
   specify an input surface directory

Required Output Arguments:

 --output <fn>
   specify an output measure filename

Author:

 Ryan Cabeen

TableCat

Name:

 TableCat

Description:

 Concatenate the rows of two tables.  By default, it will only include fields
 that are common to both input tables.

Optional Input Arguments:

--x
input first table --y
input second table Optional Parameter Arguments: --outer include all possible fields Required Output Arguments: --output
output table Author: Ryan Cabeen

TableConvert

Name:

 TableConvert

Description:

 Convert a table between file formats

Required Input Arguments:

--input
input table Required Output Arguments: --output
output table Author: Ryan Cabeen

TableMapMath

Name:

 TableMapMath

Description:

 Evaluate an expression with a map (a table listing name/value pairs)

Required Input Arguments:

--input
the input table map Optional Parameter Arguments: --expression <String> the expression to evaluate (Default: x > 0.5) --name <String> the field name for the name (Default: name) --value <String> the field name for the value (Default: value) --result <String> the name of the result (Default: result) Required Output Arguments: --output
output table Author: Ryan Cabeen

TableMath

Name:

 TableMath

Description:

 Evaluate an expression for each row of a table

Required Input Arguments:

--input
the input table Optional Parameter Arguments: --expression <String> the expression to evaluate (Default: x > 0.5) --result <String> the field name for the result (Default: result) --na <String> the string used for invalid values (Default: NA) Required Output Arguments: --output
output table Author: Ryan Cabeen

TableMerge

Name:

 TableMerge

Description:

 Merge two tables based the value of a shared field

Required Input Arguments:

--left
input left table --right
input right table Optional Parameter Arguments: --field <String> the common field to merge on (Default: name) Required Output Arguments: --output
output table Author: Ryan Cabeen

TableNarrow

Name:

 TableNarrow

Description:

 Narrow a table to reduce the number of fields

Required Input Arguments:

--input
input table Optional Parameter Arguments: --name <String> the new field for each field name (Default: name) --value <String> the new field for each field value (Default: value) --keep <String> fields to keep (comma separated) Required Output Arguments: --output
output table Author: Ryan Cabeen

TableOutliers

Name:

 TableOutliers

Description:

 Compute z-scores to detect outliers in a table

Required Input Arguments:

--input
input table Required Output Arguments: --output
output table Author: Ryan Cabeen

TablePrintInfo

Name:

 TablePrintInfo

Description:

 Print basic information about a table

Required Input Arguments:

--input
the input table Author: Ryan Cabeen

TableSelect

Name:

 TableSelect

Description:

 Select columns from a table

Required Input Arguments:

--input
input table Optional Parameter Arguments: --where <String> an predicate for selecting records (using existing field names) --name <String> the name variable for use in the select predicate (Default: name) --select <String> an predicate for selecting fields (using the value of name) --sort <String> sort by fields (e.g. field2,#field3,^#field1 --include <String> include only specific fields (comma delimited) --exclude <String> exclude specific fields (comma delimited) --as <String> an renaming of fields (e.g. newfield=oldfield) --constant <String> add a constant field (e.g. newfield=value,newfield2=value2) Required Output Arguments: --output
output table Author: Ryan Cabeen

TableStats

Name:

 TableStats

Description:

 Compute summary statistics of a field of a table

Required Input Arguments:

--input
input table Optional Parameter Arguments: --value <String> the field to summarize (Default: value) --group <String> fields to group records by (comma separated) Required Output Arguments: --output
output table Author: Ryan Cabeen

TableVolume

Name:

 TableVolume

Description:

 Map tabular data to a volume

Required Input Arguments:

--input
input table --reference <Mask> a reference mask Optional Parameter Arguments: --vector read vector values --voxel <String> index (Default: index) --value <String> value (Default: value) --na <double> a value to substitute for NAs (Default: 0.0) Required Output Arguments: --output <Volume> output volume Author: Ryan Cabeen

TableWiden

Name:

 TableWiden

Description:

 Widen a table to expand a single field to many

Required Input Arguments:

--input
input table Optional Parameter Arguments: --name <String> the field name to expand (Default: name) --value <String> the field value to expand (Default: value) --pattern <String> pattern for joining names (Default: %s.%s) --include <String> include fields --exclude <String> exclude fields Required Output Arguments: --output
output table Author: Ryan Cabeen

TablesCat

Name:

 TablesCat

Description:

 concatentate rows of a collection of tables

Required Input Arguments:

 --input <Table(s)>
   the input tables

Optional Parameter Arguments:

 --outer
   include all possible fields

Required Output Arguments:

--output
specify the output tables Author: Ryan Cabeen

TablesMerge

Name:

 TablesMerge

Description:

 merge the fields of a collection of tables

Required Input Arguments:

 --input <Table(s)>
   the input tables

Optional Parameter Arguments:

 --field <String>
   the common field to merge on (Default: name)

Required Output Arguments:

--output
specify the output table Author: Ryan Cabeen

VectsAlignAxis

Name:

 VectsAlignAxis

Description:

 Compute an affine transform to align a set of points to the z-axis

Required Input Arguments:

 --input <Vects>
   input vects (should be roughly linear

Required Output Arguments:

 --output <Affine>
   output affine transform

Author:

 Ryan Cabeen

VectsBox

Name:

 VectsBox

Description:

 Get the bounding box of vects

Required Input Arguments:

 --input <Vects>
   input vects

Required Output Arguments:

 --output <Solids>
   output bounding box

Author:

 Ryan Cabeen

VectsCat

Name:

 VectsCat

Description:

 Concatenate two sets of vectors into one

Required Input Arguments:

 --input <Vects>
   input vects
 --cat <Vects>
   vects to concatenate

Optional Parameter Arguments:

 --dims
   concatenate dimensions (instead of vects)

Required Output Arguments:

 --output <Vects>
   output concatenated vects

Author:

 Ryan Cabeen

VectsClusterKMeans

Name:

 VectsClusterKMeans

Description:

 Cluster vects using k-means or DP-means clustering

Required Input Arguments:

 --input <Vects>
   the input vects

Optional Parameter Arguments:

 --k <Integer>
   none (Default: 3)
 --lambda <Double>
   none
 --maxiter <Integer>
   none (Default: 300)

Optional Output Arguments:

 --centers <Vects>
   the output cluster centeres
 --output <Vects>
   the output clustered vects (last coordinate stores label)

Author:

 Ryan Cabeen

VectsConvert

Name:

 VectsConvert

Description:

 Convert vects between file formats

Required Input Arguments:

 --input <Vects>
   input vects

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

VectsCreate

Name:

 VectsCreate

Description:

 Create vects

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

VectsCreateSphere

Name:

 VectsCreateSphere

Description:

 Create vects that lie on a sphere

Optional Parameter Arguments:

 --subdiv <int>
   the number of subdivisions (Default: 3)
 --hemi
   only create points on a hemisphere

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

VectsHull

Name:

 VectsHull

Description:

 Compute the convex hull of vects

Required Input Arguments:

 --input <Vects>
   input vects

Required Output Arguments:

 --output <Mesh>
   output convex hull

Author:

 Ryan Cabeen

Citation:

 Barber, C. B., Dobkin, D. P., & Huhdanpaa, H. (1996). The quickhull algorithm
 for convex hulls. ACM Transactions on Mathematical Software (TOMS), 22(4),
 469-483.

VectsJitter

Name:

 VectsJitter

Description:

 Jitter vects with isotropic Gaussian random displacements

Required Input Arguments:

 --input <Vects>
   input vects

Optional Parameter Arguments:

 --multiplier <int>
   the number of multiples to include (Default: 1)
 --std <double>
   the number of samples to take (Default: 1.0)

Required Output Arguments:

 --output <Vects>
   output subsampled vects

Author:

 Ryan Cabeen

VectsMath

Name:

 VectsMath

Description:

 Evaluate an expression at each vector

Required Input Arguments:

 --input <Vects>
   the input vects

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: mean(v))

Required Output Arguments:

 --output <Vects>
   output vects

Author:

 Ryan Cabeen

VectsModeMeanShift

Name:

 VectsModeMeanShift

Description:

 Compute the positions of modes of vectors using the mean shift algorithm

Required Input Arguments:

 --input <Vects>
   input vects

Optional Parameter Arguments:

 --bandwidth <Double>
   the spatial bandwidth (Default: 1.0)
 --minshift <Double>
   the error threshold for convergence (Default: 1.0E-6)
 --maxiter <Integer>
   the maximum number of iterations (Default: 10000)

Required Output Arguments:

 --masses <Vects>
   output masses
 --modes <Vects>
   output modes

Author:

 Ryan Cabeen

Citation:

 Comaniciu, D., & Meer, P. (2002). Mean shift: A robust approach toward
 feature space analysis. IEEE Transactions on pattern analysis and machine
 intelligence, 24(5), 603-619.

VectsPCA

Name:

 VectsPCA

Description:

 Perform principal component analysis on vects

Required Input Arguments:

 --input <Vects>
   the input vects

Optional Parameter Arguments:

 --top <Integer>
   none

Optional Output Arguments:

 --mean <Vects>
   the output mean vect
 --comps <Vects>
   the output principal components
 --vals <Vects>
   the output principal values
 --output <Vects>
   the output transformed vects

Author:

 Ryan Cabeen

VectsPrintInfo

Name:

 VectsPrintInfo

Description:

 Print basic information about vectors

Required Input Arguments:

 --input <Vects>
   the input vects

Optional Parameter Arguments:

 --stats
   print statistics
 --norm
   print statistics of vect norms

Author:

 Ryan Cabeen

VectsReduce

Name:

 VectsReduce

Description:

 Reduce the number of vectors in either a random or systematic way

Required Input Arguments:

 --input <Vects>
   input vects

Optional Parameter Arguments:

 --num <Integer>
   the maxima number of samples
 --which <String>
   the list of indices to select
 --exclude <String>
   the list of indices to exclude

Required Output Arguments:

 --output <Vects>
   output subsampled vects

Author:

 Ryan Cabeen

VectsRegisterLinear

Name:

 VectsRegisterLinear

Description:

 Estimate a linear transform to register a given pair of vects.  You can
 choose one of several methods to specify the degrees of freedom of the
 transform and how the transform parameters are estimated

Required Input Arguments:

 --source <Vects>
   input source vects
 --dest <Vects>
   input dest vects (should match source)

Optional Input Arguments:

 --weights <Vects>
   input weights (only available for some methods)

Optional Parameter Arguments:

 --method <VectsRegisterLinearMethod>
   the registration method (each has different degrees of freedom and
   estimation techniques) (Options: AffineLeastSquares, RigidDualQuaternion)
   (Default: AffineLeastSquares)

Required Output Arguments:

 --output <Affine>
   output affine transform mapping source to dest

Optional Output Arguments:

 --transformed <Vects>
   output transformed source vects (redundant, but useful for validation)

Author:

 Ryan Cabeen, Yonggang Shi

VectsRegisterRigidDualQuaternion

Name:

 VectsRegisterRigidDualQuaternion

Description:

 Estimate a rigid transform using the dual quaterionion method.  This assumes
 point-to-point correspondence between vects.

Required Input Arguments:

 --source <Vects>
   input source vects
 --dest <Vects>
   input dest vects (should match source)

Optional Input Arguments:

 --weights <Vects>
   input weights

Required Output Arguments:

 --output <Affine>
   output affine transform mapping source to dest

Optional Output Arguments:

 --transformed <Vects>
   output transformed source vects (redundant, but useful for validation)

Author:

 Ryan Cabeen, Yonggang Shi

Citation:

 Walker, Michael W., Lejun Shao, and Richard A. Volz. "Estimating 3-D location
 parameters using dual number quaternions." CVGIP: image understanding 54.3
 (1991): 358-367.

VectsSelect

Name:

 VectsSelect

Description:

 Select a which of vects

Required Input Arguments:

 --input <Vects>
   input vects

Optional Input Arguments:

 --mask <Mask>
   input mask
 --solids <Solids>
   input solids

Optional Parameter Arguments:

 --or
   use OR (instead of AND) to combine selections
 --invert
   invert the selection after combining

Required Output Arguments:

 --output <Vects>
   output selected vects

Author:

 Ryan Cabeen

VectsSpheres

Name:

 VectsSpheres

Description:

 Create spheres from vects

Required Input Arguments:

 --input <Vects>
   input vects

Optional Parameter Arguments:

 --radius <double>
   the sphere radius (Default: 1.0)

Required Output Arguments:

 --output <Solids>
   output solid spheres

Author:

 Ryan Cabeen

VectsTransform

Name:

 VectsTransform

Description:

 Transform vects

Required Input Arguments:

 --input <Vects>
   input vects

Optional Input Arguments:

 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --rows
   force rows > cols
 --cols
   force cols > rows
 --transpose
   transpose
 --subset <String>
   which the coordinates
 --flip <String>
   flip a coodinate (x, y, or z)
 --swap <String>
   swap a pair of coordinates (xy, xz, or yz)
 --perm <String>
   permute by coordinate index, e.g. 1,0,2
 --normalize
   normalize

Required Output Arguments:

 --output <Vects>
   output transformed vects

Author:

 Ryan Cabeen

VolumeActiveAxFitAMICO

Usage: qit VolumeActiveAxFitAMICO [opts]

 fit a ActiveAx volume with AMICO (https://github.com/daducci/AMICO) and

Camino (http://camino.cs.ucl.ac.uk)

Options:

 -h, --help            show this help message and exit
 --input=<file>        specify an input DWI (required)
 --gradients=<file>    specify the input gradients (7 columns required)
 --mask=<file>         specify a mask (required)
 --output=<dir>        specify an output ActiveAx directory (required)
 --which=<a,b,c,...>   specify a subset of gradients to use (comma-separated)
 --exclude=<a,b,c,...>
                       specify a subset of gradients to exclude (comma-
                       separated)
 --noflip              do not flip gradients in x
 --save                save the temporary files
 --clobber             clobber existing output

VolumeAxialFuse

Name:

 VolumeAxialFuse

Description:

 fuse volumes

Required Input Arguments:

 --input <Volume(s)>
   the input volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Optional Parameter Arguments:

 --spherical
   use input from spherical coordinates

Optional Output Arguments:

 --output-mean <Volume>
   specify the output mean volume
 --output-lambda <Volume>
   specify the output lambda volume
 --output-coherence <Volume>
   specify the output coherence volume

Author:

 Ryan Cabeen

VolumeBiTensorFit

Name:

 VolumeBiTensorFit

Description:

 Fit a bi-tensor volume to a diffusion-weighted MRI.

Required Input Arguments:

 --input <Volume>
   input diffusion-weighted MR volume
 --gradients <Gradients>
   the gradients

Optional Input Arguments:

 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --method <BiTensorFitType>
   specify an estimation method (Options: DTI, DTIFWE, Isotropic,
   FixedIsotropic, BothIsotropic, AlignedZeppelin, Zeppelin, Anisotropic)
   (Default: Isotropic)
 --cost <CostType>
   specify a cost function for non-linear fitting (Options: SE, MSE, RMSE,
   NRMSE, CHISQ, RLL) (Default: SE)
 --shells <String>
   specify a subset of gradient shells to include (comma-separated list of
   b-values)
 --which <String>
   specify a subset of gradients to include (comma-separated list of indices
   starting from zero)
 --exclude <String>
   specify a subset of gradients to exclude (comma-separated list of indices
   starting from zero)
 --threads <int>
   the number of threads to use (Default: 1)

Required Output Arguments:

 --output <Volume>
   output bitensor volume (name output like *.bti and an directory of volumes
   will be created)

Author:

 Ryan Cabeen

VolumeBiTensorReduce

Name:

 VolumeBiTensorReduce

Description:

 Reduce a bitensor volume to a single tensor volume

Required Input Arguments:

 --input <Volume>
   input bitensor volume

Optional Parameter Arguments:

 --fluid
   return the fluid compartment (default is the tissue compartment)
 --threads <int>
   the number of threads to use (Default: 1)

Required Output Arguments:

 --output <Volume>
   output tensor volume

Author:

 Ryan Cabeen

VolumeBlockRead

Name:

 VolumeBlockRead

Description:

 compose blocks into a volume

Required Input Arguments:

 --input <Pattern>
   the input pattern (e.g. volume%d.nii.gz
 --ref <Volume>
   the reference volume

Optional Parameter Arguments:

 --i <Integer>
   the i block size
 --j <Integer>
   the j block size
 --k <Integer>
   the k block size (Default: 1)

Required Output Arguments:

 --output <Volume>
   specify the output volume

Author:

 Ryan Cabeen

VolumeBlockWrite

Name:

 VolumeBlockWrite

Description:

 decompose a volume into blocks

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --i <Integer>
   the i block size
 --j <Integer>
   the j block size
 --k <Integer>
   the k block size (Default: 1)

Required Output Arguments:

 --output <Pattern>
   specify the output pattern (e.g. output%d.nii.gz)

Author:

 Ryan Cabeen

VolumeBox

Name:

 VolumeBox

Description:

 Compute the bounding box of a volume

Required Input Arguments:

 --input <Volume>
   input volume

Required Output Arguments:

 --output <Solids>
   output bounding box

Author:

 Ryan Cabeen

VolumeBrainExtract

Usage: qit bet [opts]

brain extraction with FSL

Options:

 -h, --help     show this help message and exit
 --input=<fn>   the input volume
 --output=<fn>  the output mask
 --frac=<val>   the fraction threshold

VolumeCat

Name:

 VolumeCat

Description:

 Concatenate two volumes into one

Required Input Arguments:

 --input <Volume>
   input volume
 --cat <Volume>
   volume to concatenate

Optional Input Arguments:

 --mask <Mask>
   input mask

Required Output Arguments:

 --output <Volume>
   output concatenated volume

Author:

 Ryan Cabeen

VolumeConvert

Name:

 VolumeConvert

Description:

 Convert a volume to a different format (only useful on command line)

Required Input Arguments:

 --input <Volume>
   input

Optional Parameter Arguments:

 --proto
   only copy the structure, not the intensities

Required Output Arguments:

 --output <Volume>
   output

Author:

 Ryan Cabeen

VolumeCrop

Name:

 VolumeCrop

Description:

 Crop a volume down to a smaller volume (only one criteria per run)

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask
 --solids <Solids>
   some soids

Optional Parameter Arguments:

 --range <String>
   a range specification, e.g. start:end,start:end,start:end
 --thresh <Double>
   crop out the background with a given threshold
 --invert
   invert the selection
 --pad <int>
   a padding size in voxels (Default: 0)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumeDeformationCompose

Name:

 VolumeDeformationCompose

Description:

 Compose a deformation field with an affine transform

Required Input Arguments:

 --input <Volume>
   an input deformation field
 --affine <Affine>
   an affine transform

Optional Input Arguments:

 --ref <Volume>
   a reference image

Optional Parameter Arguments:

 --invert
   invert the affine transform
 --premult
   apply the affine first

Required Output Arguments:

 --output <Volume>
   output

Author:

 Ryan Cabeen

VolumeDownsample

Name:

 VolumeDownsample

Description:

 Downsample a volume.  Unlike VolumeZoom, this includes a prefiltering step
 with a triangle filter to reduce alias artifact

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --factor <Integer>
   an downsampling scaling factor (Default: 2)
 --threads <Integer>
   the number of threads in the pool (Default: 3)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumeDwiAdc

Name:

 VolumeDwiAdc

Description:

 Compute the apparent mri coefficient (ADC) of the mri signal.  The default
 output is the mean ADC, but per-gradient outputs can also be computed

Required Input Arguments:

 --input <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients

Optional Input Arguments:

 --mask <Mask>
   the input mask

Optional Parameter Arguments:

 --component
   compute the ADC for each gradient, otherwise the average will be computed

Required Output Arguments:

 --output <Volume>
   the output ADC volume

Author:

 Ryan Cabeen

VolumeDwiAverage

Name:

 VolumeDwiAverage

Description:

 Average subvolumes from diffusion MRI.  This is often used to improve the SNR
 when the scan includes repeats

Required Input Arguments:

 --dwi <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients (must match input DWI)

Optional Parameter Arguments:

 --average <String>
   a file or comma-separated list of integers specifying how the data should
   be grouped, e.g. 1,1,1,2,2,2,3,3,3,...

Required Output Arguments:

 --outputDwi <Volume>
   the output dwi volume

Optional Output Arguments:

 --outputGradients <Gradients>
   the output gradients

Author:

 Ryan Cabeen

VolumeDwiBaseline

Name:

 VolumeDwiBaseline

Description:

 Extract baseline signal statistics from a diffusion-weighted MR volume

Required Input Arguments:

 --input <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients

Optional Input Arguments:

 --mask <Mask>
   the input mask

Optional Output Arguments:

 --mean <Volume>
   the output mean baseline signal
 --median <Volume>
   the output median baseline signal
 --var <Volume>
   the output variance of baseline signal (only meaningful if there are
   multiple baselines)
 --std <Volume>
   the output standard deviation of baseline signal (only meaningful if there
   are multiple baselines)
 --cat <Volume>
   the output complete set of baseline signals
 --drift <Volume>
   the output signal drift estimates (slope, stderr, tstat, pval, sig)
   measured by percentage change

Author:

 Ryan Cabeen

Citation:

 Vos, Sjoerd B., et al. "The importance of correcting for signal drift in
 diffusion MRI." Magnetic resonance in medicine 77.1 (2017): 285-299.

VolumeDwiCorrect

Usage: qit VolumeDwiCorrect [opts]

Basic motion and eddy current correction with FSL. This will perform affine registration of each DWI to the baseline using mutual information and subsequently rotate each b-vector using the rotational component of the transform. The gradients should be in a right-handed coordinate system.

Options:

 -h, --help           show this help message and exit
 --input-dwi=<fn>     specify an input dwi
 --input-bvecs=<fn>   specify input b-vectors
 --input-bvals=<fn>   specify input b-values
 --output-dwi=<fn>    specify an output dwi
 --output-bvecs=<fn>  specify output b-vectors
 --output-bvals=<fn>  specify output b-values

VolumeDwiEstimateNoise

Name:

 VolumeDwiEstimateNoise

Description:

 Estimate the noise parameter from the baselines of a DWI

Required Input Arguments:

 --input <Volume>
   input dwi
 --gradients <Gradients>
   input gradients

Optional Input Arguments:

 --mask <Mask>
   input mask

Required Output Arguments:

 --output <Volume>
   output error volume

Author:

 Ryan Cabeen

VolumeDwiMotionEstimation

Usage: qit VolumeDwiMotionEstimation [opts]

estimate the motion in a multi-channel volume

Options:

 -h, --help     show this help message and exit
 --input=<fn>   specify the multi-channel input volume
 --cost=<str>   specify the cost function (default is mutualinfo)
 --dof=<int>    specify the degrees of freedom (default is rigid)
 --output=<dn>  specify the output directory name

VolumeDwiNormalize

Name:

 VolumeDwiNormalize

Description:

 normalize a mri weighted image volume by the baseline signal

Required Input Arguments:

 --input <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients

Optional Input Arguments:

 --mask <Mask>
   the input mask

Optional Parameter Arguments:

 --grouping <String>
   a grouping of scans with similar TE/TR
 --unit
   normalize the signal to the unit interval (divide by average baseline)

Required Output Arguments:

 --output <Volume>
   the output baseline volume

Author:

 Ryan Cabeen

VolumeDwiReduce

Name:

 VolumeDwiReduce

Description:

 Reduce the number of mri samples in a mri weighted image

Required Input Arguments:

 --dwi <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients (must match input DWI)

Optional Parameter Arguments:

 --shells <String>
   include only specific shells
 --which <String>
   include only specific gradients (comma separated zero-based indices)
 --exclude <String>
   exclude specific gradients (comma separated zero-based indices)

Required Output Arguments:

 --outputDwi <Volume>
   the output dwi volume

Optional Output Arguments:

 --outputGradients <Gradients>
   the output gradients

Author:

 Ryan Cabeen

VolumeDwiResampleGP

Name:

 VolumeDwiResampleGP

Description:

 Resample a diffusion-weighted MR volume to have a different set of gradients
 (arbitrary b-vectors and b-values)

Required Input Arguments:

 --input <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients (must match input DWI)
 --reference <Gradients>
   the gradients used for resampling

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --lambda <Double>
   the lambda parameter (controls smoothness) (Default: 0.1)
 --alpha <Double>
   the alpha parameter (controls gradient direction scaling) (Default: 1.0)
 --beta <Double>
   the beta parameter (controls gradient strength scaling) (Default: 1.0)
 --threads <Integer>
   the number of threads to use (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output resampled diffusion-weighted MR volume (will match reference
   gradients)

Author:

 Ryan Cabeen

Citation:

 Andersson, J. L., & Sotiropoulos, S. N. (2015). Non-parametric representation
 and prediction of single-and multi-shell diffusion-weighted MRI data using
 Gaussian processes. NeuroImage, 122, 166-176.

VolumeDwiResampleOutlierGP

Name:

 VolumeDwiResampleOutlierGP

Description:

 Detect and replace outliers of a diffusion-weighted MR volume using Gaussian
 Process regression.  This first detects outliers using a very smooth GP model
 and then replaces only those outliers using a more rigid GP model

Required Input Arguments:

 --input <Volume>
   the input diffusion-weighted MR volume
 --gradients <Gradients>
   the input gradients (must match input DWI)

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --outlier <Double>
   the threshold for outlier detection. this is the fractional change in
   single value from the GP prediction to qualify as an outlier (Default:
   0.35)
 --include <Double>
   the minimum fraction of gradient directions to use for outlier replacement.
    if more than this fraction are considered inliers, then interpolation will
   be used (Default: 0.75)
 --lambdaDetect <Double>
   the lambda parameter for detecting outliers (controls smoothness) (Default:
   1.0)
 --lambdaPredict <Double>
   the lambda parameter for replacing outliers (controls smoothness) (Default:
   1.0)
 --resample
   resample all signal values with reduced GP (default will only resample
   outliers)
 --alpha <Double>
   the alpha parameter (controls gradient direction scaling) (Default: 1.0)
 --beta <Double>
   the beta parameter (controls gradient strength scaling) (Default: 1.0)
 --threads <Integer>
   the number of threads to use (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output resampled diffusion-weighted MR volume (will match reference
   gradients)

Author:

 Ryan Cabeen

Citation:

 Andersson, J. L., & Sotiropoulos, S. N. (2015). Non-parametric representation
 and prediction of single-and multi-shell diffusion-weighted MRI data using
 Gaussian processes. NeuroImage, 122, 166-176.

VolumeDwiResampleSpherical

Name:

 VolumeDwiResampleSpherical

Description:

 Resample a diffusion-weighted MR volume to have a different set of gradients
 (single shell only)

Required Input Arguments:

 --input <Volume>
   the input diffusion-weighted MR volume
 --source <Gradients>
   the (original) source gradients
 --dest <Vects>
   the destination gradient directions

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --filter <String>
   specify a filtering method (linear, local, or global) (Default: linear)
 --kappa <Double>
   the lambda parameter (Default: 5.0)
 --lambda <Double>
   the lambda parameter (Default: 0.1)
 --sigma <Double>
   the sigma parameter (Default: 20.0)
 --adaptive
   use adaptive resampling

Required Output Arguments:

 --output <Volume>
   the output resampled diffusion-weighted MR volume

Author:

 Ryan Cabeen

VolumeDwiSphericalMean

Name:

 VolumeDwiSphericalMean

Description:

 Compute the spherical mean for each shell.

Required Input Arguments:

 --dwi <Volume>
   the dwi diffusion-weighted MR volume
 --gradients <Gradients>
   the (original) source gradients

Optional Input Arguments:

 --mask <Mask>
   a mask

Required Output Arguments:

 --outputDwi <Volume>
   the output resampled diffusion-weighted MR volume
 --outputBvals <Vects>
   the output b-values

Author:

 Ryan Cabeen

VolumeDwiSubsample

Name:

 VolumeDwiSubsample

Description:

 Subsample a mri weighted volume by removing channels to maximize the
 separation of gradient directions.  This is currently optimized for single
 shell data

Required Input Arguments:

 --indwi <Volume>
   the input diffusion-weighted MR volume
 --ingrad <Gradients>
   the input gradients

Optional Parameter Arguments:

 --nums <int>
   the number of baseline channels to keep (Default: 1)
 --numd <int>
   the number of diffusion-weighted channels to keep (Default: 12)

Required Output Arguments:

 --outdwi <Volume>
   the output diffusion-weighted MR volume
 --outgrad <Gradients>
   the output gradients

Author:

 Ryan Cabeen

VolumeEnhanceContrast

Name:

 VolumeEnhanceContrast

Description:

 enhance the intensitiy contrast of a given volume.  The output will have a
 range of zero to one.

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --type <VolumeEnhanceContrastType>
   the type of contrast enhancement (Options: Histogram, Ramp, Square, Root,
   Mean) (Default: Histogram)
 --bins <int>
   the number of histogram bins (Default: 1024)
 --smooth <Double>
   smooth the histogram by adding the given proportion of the total (reduces
   effect of outliers)
 --nobg
   remove background voxels
 --thresh <double>
   specify a threshold for background removal (Default: 1.0E-6)

Required Output Arguments:

 --output <Volume>
   output enhanced image

Author:

 Ryan Cabeen

VolumeExpDecayError

Name:

 VolumeExpDecayError

Description:

 Synthesize a volume from exp decay parameters

Required Input Arguments:

 --input <Volume>
   input exp decay sample volume
 --varying <Vects>
   the varying parameters
 --model <Volume>
   the exponential decay model parameter volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --method <String>
   the type of error metric (me, nme, sse, nsse, mse, nmse, rmse, nrmse)
   (Default: nrmse)

Required Output Arguments:

 --output <Volume>
   output error

Author:

 Ryan Cabeen

VolumeExpDecayFit

Name:

 VolumeExpDecayFit

Description:

 Fit an exponential decay model to volumetric data: y = alpha * exp(-beta * x)

Required Input Arguments:

 --input <Volume>
   the input dwi

Optional Input Arguments:

 --varying <Vects>
   the varying parameters values used for fitting, if not provided the start
   and step parameters are used instead
 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --method <String>
   the method for fitting (lls, wlls, nlls) (Default: wlls)
 --start <Double>
   the starting echo time (not used if you provide a varying input) (Default:
   1.0)
 --step <Double>
   the spacing between echo times (not used if you provide a varying input)
   (Default: 1.0)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output exp decay model volume

Author:

 Ryan Cabeen

VolumeExpDecaySynth

Name:

 VolumeExpDecaySynth

Description:

 Synthesize a volume from exp decay parameters

Required Input Arguments:

 --input <Volume>
   input exp decay volume
 --varying <Vects>
   the varying parameters

Optional Input Arguments:

 --mask <Mask>
   input mask

Required Output Arguments:

 --output <Volume>
   predicted output

Author:

 Ryan Cabeen

VolumeExpRecoveryError

Name:

 VolumeExpRecoveryError

Description:

 Synthesize a volume from exp recovery parameters

Required Input Arguments:

 --input <Volume>
   input exp recovery sample volume
 --varying <Vects>
   the varying parameters
 --model <Volume>
   the exponential recovery model parameter volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --method <String>
   the type of error metric (me, nme, sse, nsse, mse, nmse, rmse, nrmse)
   (Default: nrmse)

Required Output Arguments:

 --output <Volume>
   output error

Author:

 Ryan Cabeen

VolumeExpRecoveryFit

Name:

 VolumeExpRecoveryFit

Description:

 Fit an exponential recovery model to volumetric data: y = alpha * exp(-beta *
 x)

Required Input Arguments:

 --input <Volume>
   the input dwi
 --varying <Vects>
   the varying parameters values used for fitting

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output exp recovery model volume

Author:

 Ryan Cabeen

VolumeExpRecoverySynth

Name:

 VolumeExpRecoverySynth

Description:

 Synthesize a volume from exp recovery parameters

Required Input Arguments:

 --input <Volume>
   input exp recovery volume
 --varying <Vects>
   the varying parameters

Optional Input Arguments:

 --mask <Mask>
   input mask

Required Output Arguments:

 --output <Volume>
   predicted output

Author:

 Ryan Cabeen

VolumeExtrema

Name:

 VolumeExtrema

Description:

 Compute the local extrema of a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --channel <int>
   the volume channel (Default: 0)
 --minima
   find the minima
 --maxima
   find the maxima
 --element <String>
   specify an element (Default: cross)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

VolumeFibersCat

Name:

 VolumeFibersCat

Description:

 concatenate fibers volumes

Required Input Arguments:

 --input <FibersVolume(s)>
   the input fibers volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Required Output Arguments:

 --output <FibersVolume>
   specify the output fibers volume

Author:

 Ryan Cabeen

VolumeFibersError

Name:

 VolumeFibersError

Description:

 Compute error metrics between a ground truth and test fibers volume

Required Input Arguments:

 --truth <Volume>
   the truth fibers volume
 --test <Volume>
   the test fibers volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --thresh <double>
   a threshold for compartment existence (Default: 0.05)

Optional Output Arguments:

 --missing <Volume>
   output measuring number of missing compartment error
 --extra <Volume>
   output measuring number of extra compartment error
 --linehaus <Volume>
   output measuring the hausdorff angular error
 --linetotal <Volume>
   output measuring the total angular error
 --frachaus <Volume>
   output measuring the hausdorff fraction error
 --fractotal <Volume>
   output measuring the total fraction error
 --fraciso <Volume>
   output measuring the isotropic fraction error

Author:

 Ryan Cabeen

VolumeFibersFit

Name:

 VolumeFibersFit

Description:

 Fit a fibers volume using non-linear optimization.  Regularization is used to
 constrain the volume fractions.

Required Input Arguments:

 --input <Volume>
   input diffusion-weighted MR volume
 --gradients <Gradients>
   the gradients

Optional Input Arguments:

 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --comps <int>
   the number of fibers (Default: 1)
 --lambda <double>
   the regularization weight (Default: 0.001)
 --power <double>
   the regularization power (Default: 1.0)
 --cost <CostType>
   specify a cost function for non-linear fitting (Options: SE, MSE, RMSE,
   NRMSE, CHISQ, RLL) (Default: SE)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   output fibers volume

Author:

 Ryan Cabeen

VolumeFibersFitFsl

Usage: qit VolumeFibersFitFsl [opts]

 fit the ball and sticks model with FSL XFIBRES

Options:

 -h, --help            show this help message and exit
 --input=<file>        specify a dwi (required)
 --gradients=<file>    specify a gradients file (required)
 --mask=<file>         specify a mask (required)
 --output=<file>       specify an output directory (required)
 --shells=<a,b,c,...>  specify a subset of gradient shells (comma-separated)
 --which=<a,b,c,...>   specify a subset of gradients to use (comma-separated)
 --exclude=<a,b,c,...>
                       specify a subset of gradient to exclude (comma-
                       separated)
 --clobber             clobber existing output
 --fudge=<value>       specify fudge parameter in fsl xfibres
 --nj=<value>          specify nj in fsl xfibres
 --bi=<value>          specify bi in fsl xfibres
 --model=<value>       specify a model in fsl xfibres
 --se=<value>          specify se in fsl xfibres
 --upe=<value>         specify upe in fsl xfibres
 --nfibres=<value>     specify nfibres in fsl xfibres
 --seed=<value>        specify a random seed in fsl xfibres
 --nonlinear           specify nonlinear fitting in fsl xfibres
 --no-cnonlinear       specify no constrained nonlinear ftting in fsl xfibres
 --rician              specify rician noise model in fsl xfibres
 --nospat              specify no spatial fitting in fsl xfibres
 --allard              apply ARD on all compartments in fsl xfibres
 --noard               specify noard in fsl xfibres
 --f0                  use a f0 compartment in fsl xfibres
 --ardf0               use ARD with f0 in fsl xfibres

VolumeFibersFuse

Name:

 VolumeFibersFuse

Description:

 fuse a collection of fibers volumes

Required Input Arguments:

 --input <Volume(s)>
   specify the input fibers volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Optional Parameter Arguments:

 --pattern <String(s)>
   specify a list of names that will be substituted with input %s
 --estimator <String>
   specify an estimator type
 --selection <String>
   specify a selection type
 --hpos <Double>
   specify spatial bandwidth
 --support <Integer>
   specify a support size
 --lambda <Double>
   specify a lambda parameter
 --maxcomps <Integer>
   specify a maxima number of components
 --restarts <Integer>
   specify a number of restarts
 --minfrac <Double>
   specify a minima volume fraction

Required Output Arguments:

 --output <Volume>
   specify the output fibers volume

Author:

 Ryan Cabeen

VolumeFibersNoise

Name:

 VolumeFibersNoise

Description:

 Add orientation and volume fraction noise to a fibers volume

Required Input Arguments:

 --input <Volume>
   input fibers volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --line <Double>
   the sigma of the orientation noise
 --frac <Double>
   the sigma of the volume fraction noise

Required Output Arguments:

 --output <Volume>
   output noisy fibers volume

Author:

 Ryan Cabeen

VolumeFibersSmooth

Name:

 VolumeFibersSmooth

Description:

 Smooth a fibers volume

Required Input Arguments:

 --input <Volume>
   the input fibers volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --comps <int>
   a maxima number of fiber compartments (Default: 3)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output fibers volume

Author:

 Ryan Cabeen

Citation:

 Cabeen, R. P., Bastin, M. E., & Laidlaw, D. H. (2016). Kernel regression
 estimation of fiber orientation mixtures in mri MRI. NeuroImage, 127,
 158-172.

VolumeFibersTransform

Name:

 VolumeFibersTransform

Description:

 Spatially transform a fibers volume

Required Input Arguments:

 --input <Volume>
   the input fibers volume

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)
 --mask <Mask>
   input mask
 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --reorientation <ReorientationType>
   specify a reorient method (Options: FiniteStrain, Jacobian) (Default:
   Jacobian)
 --estimation <EstimationType>
   the estimation type (Options: Match, Rank) (Default: Match)
 --selection <SelectionType>
   the selection type (Options: Max, Fixed, Linear, Adaptive) (Default:
   Adaptive)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --comps <int>
   a maxima number of fiber compartments (Default: 3)
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --min <double>
   a minima volume fraction (Default: 0.01)
 --lambda <double>
   a data adaptive threshold (Default: 0.99)
 --threads <int>
   the number of threads (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output transformed volume

Author:

 Ryan Cabeen

Citation:

 Cabeen, R. P., Bastin, M. E., & Laidlaw, D. H. (2016). Kernel regression
 estimation of fiber orientation mixtures in mri MRI. NeuroImage, 127,
 158-172.

VolumeFibersZoom

Name:

 VolumeFibersZoom

Description:

 Zoom a fibers volume

Required Input Arguments:

 --input <Volume>
   the input fibers volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --factor <double>
   a zooming factor (Default: 2.0)
 --isotropic <Double>
   zoom to a given isotropic voxel size (not by a factor)
 --estimation <EstimationType>
   the estimation type (Options: Match, Rank) (Default: Match)
 --selection <SelectionType>
   the selection type (Options: Max, Fixed, Linear, Adaptive) (Default:
   Linear)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --comps <int>
   a maxima number of fiber compartments (Default: 3)
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --min <double>
   a minima volume fraction (Default: 0.01)
 --lambda <double>
   a data adaptive threshold (Default: 0.99)

Required Output Arguments:

 --output <Volume>
   the output fibers volume

Author:

 Ryan Cabeen

Citation:

 Cabeen, R. P., Bastin, M. E., & Laidlaw, D. H. (2016). Kernel regression
 estimation of fiber orientation mixtures in mri MRI. NeuroImage, 127,
 158-172.

VolumeFilterBilateral

Name:

 VolumeFilterBilateral

Description:

 Filter a volume with a bilateral filter

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --channel <Integer>
   volume channel (default applies to all)
 --hpos <Double>
   positional bandwidth (Default: 1.0)
 --hval <Double>
   data adaptive bandwidth
 --support <int>
   filter radius in voxels (filter will be 2 * support + 1 in each dimension)
   (Default: 3)
 --iterations <int>
   number of repeats (Default: 1)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

Citation:

 Elad, M. (2002). On the origin of the bilateral filter and ways to improve
 it. IEEE Transactions on image processing, 11(10), 1141-1151.

VolumeFilterDoG

Name:

 VolumeFilterDoG

Description:

 Filter a volume using a Gaussian kernel

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --support <int>
   filter support (filter will be 2 * support + 1 voxels in each dimension)
   (Default: 3)
 --low <double>
   the low smoothing level (Default: 1.0)
 --high <double>
   the low smoothing level (Default: 2.0)
 --num <int>
   number of applications (Default: 1)
 --threads <int>
   number of threads (Default: 1)
 --pass
   pass un-masked values through the filter

Required Output Arguments:

 --output <Volume>
   output mask

Author:

 Ryan Cabeen

VolumeFilterDoG$1

 No module named VolumeFilterDoG$1 was found!
 Maybe you are looking for one of these?
   VolumeFilterDoG
   VolumeFilterNLM
   VolumeFilterPDE
   VolumeFilterMedian
   VolumeFilterFrangi
   VolumeFibersZoom
   VolumeFibersFit
   VolumeFibersNoise
   VolumeFilterHessian
   VolumeFilterGaussian

VolumeFilterDoG$2

 No module named VolumeFilterDoG$2 was found!
 Maybe you are looking for one of these?
   VolumeFilterDoG
   VolumeFilterNLM
   VolumeFilterPDE
   VolumeFilterMedian
   VolumeFilterFrangi
   VolumeFibersZoom
   VolumeFibersFit
   VolumeFibersNoise
   VolumeFilterHessian
   VolumeFilterGaussian

VolumeFilterDoG$3

 No module named VolumeFilterDoG$3 was found!
 Maybe you are looking for one of these?
   VolumeFilterDoG
   VolumeFilterNLM
   VolumeFilterPDE
   VolumeFilterMedian
   VolumeFilterFrangi
   VolumeFibersZoom
   VolumeFibersFit
   VolumeFibersNoise
   VolumeFilterHessian
   VolumeFilterGaussian

VolumeFilterFrangi

Name:

 VolumeFilterFrangi

Description:

 Filter a volume using a Frangi filter.  This extracts tubular structures

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --support <int>
   filter support (filter will be 2 * support + 1 voxels in each dimension)
   (Default: 3)
 --num <int>
   number of smoothing iterations (Default: 1)
 --low <double>
   the low scale level (Default: 1.0)
 --high <double>
   the high scale level (Default: 5.0)
 --scales <int>
   the number of scale samples (Default: 5)
 --alpha <double>
   the alpha Frangi parameter (Default: 0.5)
 --beta <double>
   the beta Frangi parameter (Default: 0.5)
 --gamma <double>
   the gamma Frangi parameter for 3D structures (Default: 300.0)
 --gammaPlanar <double>
   the gamma Frangi parameter for 2D structures (Default: 15.0)
 --threads <int>
   number of threads (Default: 1)
 --dark
   use detect dark tubes instead of bright tubes
 --sobel
   use a sobel operator (default is central finite difference)
 --full
   return the full scale space (default is maximum)
 --pass
   pass un-masked values through the filter

Required Output Arguments:

 --output <Volume>
   output filter response

Optional Output Arguments:

 --outputScale <Volume>
   output scale of the tubular structure

Author:

 Ryan Cabeen

Citation:

 Frangi, Alejandro F., et al. "Multiscale vessel enhancement filtering."
 International Conference on Medical Image Computing and Computer-Assisted
 Intervention. Springer, Berlin, Heidelberg, 1998.

VolumeFilterGaussian

Name:

 VolumeFilterGaussian

Description:

 Filter a volume using a Gaussian kernel

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --support <int>
   filter support (filter will be 2 * support + 1 voxels in each dimension)
   (Default: 3)
 --sigma <double>
   the smoothing level (Default: 1.0)
 --num <int>
   number of applications (Default: 1)
 --threads <int>
   number of threads (Default: 1)
 --full
   use a full convolution filter (otherwise separate filters are used)
 --pass
   pass un-masked values through the filter
 --channel <Integer>
   the volume channel (default applies to all)

Required Output Arguments:

 --output <Volume>
   output mask

Author:

 Ryan Cabeen

VolumeFilterGradient

Name:

 VolumeFilterGradient

Description:

 Filter a volume to compute its Hessian

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --threads <int>
   number of threads (Default: 1)
 --sobel
   use a sobel operator (default is central finite difference)
 --mag
   return the gradient magnitude

Required Output Arguments:

 --output <Volume>
   output mask

Author:

 Ryan Cabeen

VolumeFilterHessian

Name:

 VolumeFilterHessian

Description:

 Filter a volume to compute its Hessian

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --threads <int>
   number of threads (Default: 1)
 --sobel
   use a sobel operator (default is central finite difference)
 --eig
   return the eigenvalues (exclusive with det and norm flags)
 --det
   return the determinant (exclusive with eig and norm flags)
 --norm
   return the Frobenius norm (exclusive with the eig and det flag)

Required Output Arguments:

 --output <Volume>
   output mask

Author:

 Ryan Cabeen

VolumeFilterHessian$1

 No module named VolumeFilterHessian$1 was found!
 Maybe you are looking for one of these?
   VolumeFilterHessian
   VolumeFilterGaussian
   VolumeFilterMedian
   VolumeFilterGradient
   VolumeFilterTriangle
   VolumeFilterFrangi
   VolumeFilterMeanShift
   VolumeFibersFit
   VolumeFilterDoG
   VolumeFilterBilateral

VolumeFilterMeanShift

Name:

 VolumeFilterMeanShift

Description:

 Process a volume with mean shift analysis for either anisotropic filtering or
 segmentation

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --hpos <double>
   the spatial bandwidth in mm (Default: 8.0)
 --hval <double>
   the adaptive bandwidth in units of intensity (Default: 64.0)
 --iters <int>
   the maxima number of iterations (Default: 5000)
 --minshift <double>
   the threshold for stopping gradient updates (Default: 0.001)
 --minsize <double>
   the minima cluster size (Default: 50.0)

Optional Output Arguments:

 --filtered <Volume>
   the output filtered image
 --segmented <Mask>
   the output segmentation

Author:

 Ryan Cabeen

Citation:

 Comaniciu, D., & Meer, P. (2002). Mean shift: A robust approach toward
 feature space analysis. IEEE Transactions on pattern analysis and machine
 intelligence, 24(5), 603-619.

VolumeFilterMedian

Name:

 VolumeFilterMedian

Description:

 Filter a volume using a median filter

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --window <int>
   the window size in voxels (Default: 1)
 --channel <Integer>
   the volume channel (default applies to all)
 --slice <String>
   restrict the filtering to a specific slice (i, j, or k)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeFilterNLM

Name:

 VolumeFilterNLM

Description:

 Apply a non-local means filter to a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask
 --noise <Volume>
   a volume specifying the noise level h for each voxel
 --bgmask <Mask>
   use a background mask for estimating h (standard deviation of signal)
 --bgsolids <Solids>
   us a background geometric solid for estimating h (standard deviation of
   signal)

Optional Parameter Arguments:

 --channel <Integer>
   the volume channel (default applies to all)
 --slice <String>
   restrict the filtering to a specific slice (i, j, or k)
 --patch <int>
   the patch size (Default: 1)
 --block <int>
   the block size (Default: 10)
 --h <double>
   the noise level (Default: 1.0)
 --adaptive
   whether an adaptive noise model should be used
 --rician
   whether a Rician noise model should be used
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

Citation:

 P. Coupe, P. Yger, S. Prima, P. Hellier, C. Kervrann, C. Barillot, An
 Optimized Blockwise Non Local Means Denoising Filter for 3D Magnetic
 Resonance Images, IEEE Transactions on Medical Imaging, 27(4):425-441, 2008

VolumeFilterPDE

Name:

 VolumeFilterPDE

Description:

 Filter a volume using a PDE representing anisotropic mri

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --channel <String>
   the volume channel(s) (default applies to all)
 --lambda <Double>
   smoothing parameter (in mm) (Default: 0.16666666666666666)
 --k <Double>
   anisotropic flux parameter (relative to image intensities) (Default: 0.01)
 --steps <Integer>
   the number of timesteps to apply (Default: 5)
 --anisotropic
   use anisotropic smoothing
 --quadratic
   use a quadratic flux (instead of exponential)
 --recurse
   use the output as input

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

Citation:

 Perona, P., & Malik, J. (1990). Scale-space and edge detection using
 anisotropic mri. IEEE Transactions on pattern analysis and machine
 intelligence, 12(7), 629-639.

VolumeFilterTriangle

Name:

 VolumeFilterTriangle

Description:

 Filter a volume using a Triangle kernel

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --support <int>
   filter support (filter will be 2 * support + 1 in each dimension) (Default:
   3)
 --num <int>
   number of applications (Default: 1)
 --pass
   pass un-masked values through the filter
 --channel <Integer>
   the volume channel (default applies to all)

Required Output Arguments:

 --output <Volume>
   output mask

Author:

 Ryan Cabeen

VolumeFlip

Name:

 VolumeFlip

Description:

 Flip the voxel values of volume along coordinate axes

Required Input Arguments:

 --input <Volume>
   input volume

Optional Parameter Arguments:

 --i
   flip in i
 --j
   flip in j
 --k
   flip in k

Required Output Arguments:

 --output <Volume>
   output volume

Optional Output Arguments:

 --xfm <Affine>
   output spatial affine transform for the flip
 --invxfm <Affine>
   output spatial inverse affine transform for the flip

Author:

 Ryan Cabeen

VolumeFlip$1

 No module named VolumeFlip$1 was found!
 Maybe you are looking for one of these?
   VolumeFlip
   VolumeSlice
   VolumeTile
   VolumeNoise
   VolumeCrop
   VolumeOrigin
   VolumeDwiAdc
   VolumeReduce
   VolumeRender
   VolumeOdfFit

VolumeFloodFill

Name:

 VolumeFloodFill

Description:

 Flip the voxel values of volume along coordinate axes

Required Input Arguments:

 --input <Volume>
   input volume of values for filling
 --source <Mask>
   a mask indicating the source, i.e. which voxels of the input are used for
   filling

Optional Input Arguments:

 --dest <Mask>
   a mask used for restricting the voxel flooded (must be convex, but this is
   not checked)

Optional Parameter Arguments:

 --fix <int>
   maximum number of fixing passes (Default: 0)

Required Output Arguments:

 --outputFlood <Volume>
   output volume of flood values

Optional Output Arguments:

 --outputDist <Volume>
   output distance field

Author:

 Ryan Cabeen

VolumeFuse

Name:

 VolumeFuse

Description:

 fuse volumes

Required Input Arguments:

 --input <Volume(s)>
   the input volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Optional Parameter Arguments:

 --pattern <String(s)>
   specify a list of names that will be substituted with input %s
 --bg <Double>
   specify an additional background value for softmax or sumnorm
 --gain <Double>
   specify a gain for softmax
 --offset <Double>
   specify a offset for softmax

Optional Output Arguments:

 --output-cat <Volume>
   specify the output concatenated volume
 --output-min <Volume>
   specify the output min volume
 --output-max <Volume>
   specify the output max volume
 --output-sum <Volume>
   specify the output sum volume
 --output-mean <Volume>
   specify the output mean volume
 --output-var <Volume>
   specify the output var volume
 --output-std <Volume>
   specify the output std volume
 --output-cv <Volume>
   specify the output cv volume
 --output-softmax <Volume>
   specify the output softmax
 --output-sumnorm <Volume>
   specify the output sumnorm

Author:

 Ryan Cabeen

VolumeGradient

Name:

 VolumeGradient

Description:

 Compute the gradient of an image

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --channel <Integer>
   the volume channel (default applies to all) (Default: 0)
 --type <String>
   type of finite difference approximation (forward, backward, central)
   (Default: central)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeGradientMagnitude

Name:

 VolumeGradientMagnitude

Description:

 Compute the gradient magnitude of an image

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --channel <Integer>
   the volume channel (default applies to all) (Default: 0)
 --type <String>
   type of finite difference approximation (forward, backward, central)
   (Default: central)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeIsotropic

Name:

 VolumeIsotropic

Description:

 Isotropically scale a volume

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --size <double>
   the output voxel size (Default: 1.0)
 --interp <InterpolationType>
   an interpolation type (Options: Nearest, Trilinear, Tricubic, Gaussian,
   GaussianLocalLinear, GaussianLocalQuadratic) (Default: Tricubic)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumeJacobian

Name:

 VolumeJacobian

Description:

 Compute the jacobian of a deformation volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask
 --affine <Affine>
   optional affine component to remove

Optional Parameter Arguments:

 --deformation
   treat the input as a deformation (i.e. displacement)
 --eigenvalues
   return the eigenvalues (exclusive with determinant flag)
 --determinant
   return the determinant (exclusive with eigenvalues flag)
 --logarithm
   return the logarithm (works with other options)

Required Output Arguments:

 --output <Volume>
   output table

Author:

 Ryan Cabeen

VolumeKurtosisFit

Name:

 VolumeKurtosisFit

Description:

 Fit a kurtosis volume.  Warning: this does not yet estimate the kurtosis
 indices, e.g. FA, MK, etc.

Required Input Arguments:

 --input <Volume>
   input diffusion-weighted MR volume
 --gradients <Gradients>
   the gradients

Optional Input Arguments:

 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --method <KurtosisFitType>
   specify an estimation method, (FW enables free water elimination) (Options:
   LLS, WLLS, FWLLS, FWWLLS) (Default: LLS)
 --shells <String>
   specify a subset of gradient shells to include (comma-separated list of
   b-values)
 --which <String>
   specify a subset of gradients to include (comma-separated list of indices
   starting from zero)
 --exclude <String>
   specify a subset of gradients to exclude (comma-separated list of indices
   starting from zero)
 --threads <int>
   the number of threads to use (Default: 1)

Required Output Arguments:

 --output <Volume>
   output kurtosis volume

Author:

 Ryan Cabeen

Citation:

 Veraart, J., Sijbers, J., Sunaert, S., Leemans, A., Jeurissen, B.: Weighted
 linear least squares estimation of mri mri parameters: strengths,
 limitations, and pitfalls. NeuroImage 81 (2013) 335-346

VolumeKurtosisFitMatlab

Usage: qit VolumeKurtosisFitMatlab [opts]

 fit a diffusion kurtosis model using the package at https://github.com/NYU-

DiffusionMRI/Diffusion-Kurtosis-Imaging

Options:

 -h, --help            show this help message and exit
 --input=<file>        specify an input DWI (required)
 --gradients=<file>    specify the input gradients (required)
 --mask=<file>         specify a mask (required)
 --output=<fn>         specify an output kurtosis volume (required)
 --shells=<a,b,c,...>  specify a subset of gradient shells (comma-separated)
 --which=<a,b,c,...>   specify a subset of gradients to use (comma-separated)
 --exclude=<a,b,c,...>
                       specify a subset of gradients to exclude (comma-
                       separated)
 --noflip              do not flip gradients in x
 --save                save the temporary files
 --clobber             clobber existing output

VolumeKurtosisODF

Name:

 VolumeKurtosisODF

Description:

 Sample an orientation distribution function (ODF) from a kurtosis volume.

Required Input Arguments:

 --input <Volume>
   the input kurtosis volume
 --dirs <Vects>
   the sphere directions

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --alpha <Double>
   the alpha power value (Default: 10.0)
 --detail <Integer>
   the level of detail for spherical ODF sampling (Default: 4)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output odf volume

Author:

 Ryan Cabeen

VolumeKurtosisPeaks

Name:

 VolumeKurtosisPeaks

Description:

 Extract the peaks from a kurtosis volume.  This finds the average direction
 of local maxima clustered by hierarchical clustering.  The output fibers will
 encode the peak ODF value in place of volume fraction.

Required Input Arguments:

 --input <Volume>
   the input kurtosis volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --comps <Integer>
   the maximum number of comps (Default: 3)
 --alpha <Double>
   the alpha power value (Default: 10.0)
 --thresh <Double>
   the minimum peak threshold (Default: 0.0)
 --detail <Integer>
   the level of detail for spherical ODF sampling (Default: 4)
 --cluster <Double>
   the minimum angle in degrees for hierarchical clustering of local maxima
   (Default: 5.0)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output fibers volume

Author:

 Ryan Cabeen

VolumeMarchingCubes

Name:

 VolumeMarchingCubes

Description:

 Extract a mesh from a volume level set.  This can be used for extracting
 boundary surfaces of distance fields, probability maps, parametric maps, etc.
  The background level should be changed depending on the context though to
 make sure the mesh orientation is correct.

Required Input Arguments:

 --input <Volume>
   input volume

Optional Parameter Arguments:

 --level <double>
   level set to extract (Default: 0.5)
 --background <double>
   background value for outside sampling range (should be zero if the
   background is 'black' and a large number if the input is similar to a
   distance field) (Default: 0.0)

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

Citation:

 Lorensen, W. E., & Cline, H. E. (1987, August). Marching cubes: A high
 resolution 3D surface construction algorithm. In ACM SIGGRAPH Computer
 Graphics (Vol. 21, No. 4, pp. 163-169)

VolumeMarchingSquares

Name:

 VolumeMarchingSquares

Description:

 Extract isocontours from slices of a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Parameter Arguments:

 --level <double>
   level set to extract (Default: 0.0)
 --background <double>
   background value for outside sampling range (Default:
   1.7976931348623157E308)
 --dim <String>
   volume channel to contour (x, y, or z) (Default: z)
 --start <int>
   starting slice index (Default: 0)
 --step <int>
   number of slices between contours (Default: 1)

Required Output Arguments:

 --output <Curves>
   output contours

Author:

 Ryan Cabeen

Citation:

 Maple, C. (2003, July). Geometric design and space planning using the
 marching squares and marching cube algorithms. In Geometric Modeling and
 Graphics, 2003. Proceedings. 2003 International Conference on (pp. 90-95).
 IEEE.

VolumeMask

Name:

 VolumeMask

Description:

 Mask a volume

Required Input Arguments:

 --input <Volume>
   input volume
 --mask <Mask>
   a mask

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeMaxProb

Name:

 VolumeMaxProb

Description:

 Find the maxima probability labels

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask to indicate background

Optional Parameter Arguments:

 --bglabel <int>
   the background label (Default: 0)
 --bgvalue <double>
   the background value (Default: 1.0)

Optional Output Arguments:

 --labels <Mask>
   output mask of the extremal index
 --values <Volume>
   output volume of the extremal values

Author:

 Ryan Cabeen

VolumeMeasure

Name:

 VolumeMeasure

Description:

 Collect statistical sumaries of a volume using a mask.  This supports single
 label masks and more advanced options for multi-channel masks (e.g. loading
 names associated with each label)

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask
--lookup
use a lookup for region names Optional Parameter Arguments: --background use the background --multiple use multiple regions --channel <int> specify a volume channel (Default: 0) --base <String> specify a region basename (Default: region) --index <String> specify the lookup index field (Default: index) --name <String> specify the lookup name field (Default: name) --region <String> specify the output region field name (Default: region) --stat <String> specify the output statistic field name (Default: name) --value <String> specify the output value field name (Default: value) Required Output Arguments: --output
output table Author: Ryan Cabeen

VolumeMeasureBatch

Name:

 VolumeMeasureBatch

Description:

 Compute measures of a set of volumes in batch mode.

Required Input Arguments:

 --mask <FilePattern>
   specify an mask filename pattern

Required Parameter Arguments:

 --names <Spec>
   specify bundle identifiers

Optional Parameter Arguments:

 --density
   measure density from input mask
 --thresh <Double>
   specify a density threshold for volumetry (Default: 0.5)
 --volume <String=Volume> [...]
   specify volumes to sample

Required Output Arguments:

 --output <Directory>
   specify an output directory

Author:

 Ryan Cabeen

VolumeModelError

Name:

 VolumeModelError

Description:

 Compute the root mean square error between a model and dwi volume

Required Input Arguments:

 --input <Volume>
   input model volume
 --dwi <Volume>
   input dwi
 --gradients <Gradients>
   input gradients

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --model <String>
   a model name (default will try to detect it)
 --type <ModelErrorType>
   specify an error type (default is root mean square error) (Options: MSE,
   RMSE, NRMSE, CHISQ, RCHISQ, RLL, BIC, AIC) (Default: RMSE)
 --dof <Integer>
   specify an specific degrees of freedom (useful for models that were
   constrained when fitting)
 --noise <Double>
   specify an noise level (used for chisq, rll, bic).  otherwise, noise is
   estimated from multiple baselines for each voxel

Required Output Arguments:

 --output <Volume>
   output error volume

Author:

 Ryan Cabeen

VolumeModelFeature

Name:

 VolumeModelFeature

Description:

 Extract a feature from a model volume

Required Input Arguments:

 --input <Volume>
   input model volume

Optional Parameter Arguments:

 --model <String>
   a model name (default will try to detect it)
 --feature <String>
   a feature name (Default: FA)

Required Output Arguments:

 --output <Volume>
   output feature volume

Author:

 Ryan Cabeen

VolumeModelReorient

Name:

 VolumeModelReorient

Description:

 Reorient the fiber orientations of a model volume.  If both a flip and swap
 are specified, the flip is performed first. This only works for tensor,
 noddi, and fibers volumes

Required Input Arguments:

 --input <Volume>
   input model volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --model <String>
   a model name (default will try to detect it)
 --flip <String>
   flip a coodinate (x, y, z, or none)
 --swap <String>
   swap a pair of coordinates (xy, xz, yz, or none)

Required Output Arguments:

 --output <Volume>
   output error volume

Author:

 Ryan Cabeen

VolumeModelSample

Name:

 VolumeModelSample

Description:

 Sample model parameters based on a variety of possible data objects

Required Input Arguments:

 --input <Volume>
   the input model volume

Optional Input Arguments:

 --vects <Vects>
   vects storing the position where models should be sampled
 --solids <Solids>
   solids storing the position where models should be sampled
 --mask <Mask>
   mask storing the position where models should be sampled
 --curves <Curves>
   curves storing the position where models should be sampled
 --mesh <Mesh>
   mesh storing the position where models should be sampled

Optional Parameter Arguments:

 --model <ModelType>
   a model type (if you select None, the code will try to detect it) (Options:
   None, Tensor, BiTensor, Fibers, Spharm, Kurtosis, Noddi, ActiveAx,
   ExpDecay) (Default: None)
 --jitter <Double>
   jitter the samples by a given amount
 --cull <Double>
   cull the samples at a given threshold ditance
 --multiplier <Integer>
   a multiplier of the number of samples taken (sometimes only makes sense
   when jittering) (Default: 1)
 --limit <Integer>
   a maximum number of samples (the excess is randomly selected)
 --param
   samples should store only model parameters (otherwise the position is
   prepended)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --support <Integer>
   the interpolation filter radius in voxels (Default: 5)
 --hpos <Double>
   the positional interpolation bandwidth in mm (Default: 1.5)
 --comps <int>
   a maxima number of compartments (xfib only) (Default: 3)
 --log
   use log-euclidean estimation (dti only)
 --threads <int>
   the number of threads (Default: 4)

Required Output Arguments:

 --output <Vects>
   the output sampled vects

Author:

 Ryan Cabeen

Citation:

 Cabeen, R. P., Bastin, M. E., & Laidlaw, D. H. (2016). Kernel regression
 estimation of fiber orientation mixtures in mri MRI. NeuroImage, 127,
 158-172.

VolumeModelSynth

Name:

 VolumeModelSynth

Description:

 Synthesize a dMRI from a fibers volume

Required Input Arguments:

 --input <Volume>
   input model volume
 --gradients <Gradients>
   the gradient scheme

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --model <String>
   a model name (default will try to detect it)

Required Output Arguments:

 --output <Volume>
   output synthesized diffusion-weighted MR volume

Author:

 Ryan Cabeen

VolumeModelTrackStreamline

Name:

 VolumeModelTrackStreamline

Description:

 Perform deterministic multi-fiber streamline tractography from a model
 volume.  This supports tensor, fibers, spharm, and noddi volumes.

Required Input Arguments:

 --input <Volume>
   the input model volume

Optional Input Arguments:

 --seedVects <Vects>
   seed from vects
 --seedMask <Mask>
   a seed mask (one seed per voxel is initiated from this)
 --seedSolids <Solids>
   seed from solids (one seed per object is initiated from this)
 --includeMask <Mask>
   an include mask (curves are only included if they touch this, i.e. AND)
 --includeSolids <Solids>
   an include solids (curves are only included if they touch this, i.e. AND)
 --includeAddMask <Mask>
   an additional include mask (curves are only included if they touch this,
   i.e. AND)
 --includeAddSolids <Solids>
   an additional include solids (curves are only included if they touch this,
   i.e. AND)
 --excludeMask <Mask>
   an exclude mask (curves are removed if they touch this mask, i.e. NOT)
 --excludeSolids <Solids>
   an exclude solids object (curves are removed if they touch any solid, ie.e
   NOT)
 --trapMask <Mask>
   a trap mask (tracking terminates when leaving this mask)
 --trapSolids <Solids>
   a trap solids object  (tracking terminates when leaving any solid)
 --stopMask <Mask>
   a stop mask (tracking terminates when reaching this mask)
 --stopSolids <Solids>
   a stop solids object  (tracking terminates when reaching any solid)
 --endMask <Mask>
   an endpoint mask (curves are only retained if they end inside this)
 --endSolids <Solids>
   an endpoint solids object (curves are only retained if they end inside
   this)
 --trackMask <Mask>
   a tracking mask (tracking is stopped if a curve exits this mask)
 --trackSolids <Solids>
   a tracking solids (tracking is stopped if a curve exits solids)

Optional Parameter Arguments:

 --model <String>
   a model name (default will try to detect it)
 --samples <Integer>
   the number of samples per seed object (e.g. voxels, spheres, boxes, etc)
   (Default: 1)
 --angle <Double>
   the angle stopping criteria (maximum change in orientation per step)
   (Default: 45.0)
 --step <Double>
   the step size for tracking (Default: 1.0)
 --min <double>
   a minima value for tracking (FA for dti, frac for xfib/spharm, ficvf for
   noddi) (Default: 0.075)
 --length <Double>
   the minimum streamline length (Default: 0.0)
 --limitSeeds <Integer>
   a maximum number of seeds (Default: 2000000)
 --limitTracks <Integer>
   a maximum number of tracks (Default: 2000000)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Nearest)
 --rk
   use fourth-order Runge-Kutta integration (default is Euler)
 --multi
   use probabilistic multi-fiber selection (xfib/spharm only)
 --mono
   use monodirectional seeding (default is bidirectional)
 --or
   take the logical OR instead of AND when applicable
 --threads <int>
   the number of threads (Default: 3)
 --pascal
   use pascal modeling (recursively performs tractography, fits the model, and
   then tracks again with the model)

Required Output Arguments:

 --output <Curves>
   the output tractography curves

Author:

 Ryan Cabeen

Citation:

 Cabeen, R. P., Bastin, M. E., & Laidlaw, D. H. (2016). Kernel regression
 estimation of fiber orientation mixtures in mri MRI. NeuroImage, 127,
 158-172.

VolumeModelTrackStreamline$1

 No module named VolumeModelTrackStreamline$1 was found!
 Maybe you are looking for one of these?
   VolumeModelTrackStreamline
   VolumeModelTrackQuilt
   VolumeModelSample
   VolumeModelReorient
   VolumeModelFeature
   VolumeModelSynth
   VolumeVoxelMathScalar
   VolumeModelError
   VolumeNoddiTransform
   VolumeSetSampling

VolumeModelTrackStreamline$2

 No module named VolumeModelTrackStreamline$2 was found!
 Maybe you are looking for one of these?
   VolumeModelTrackStreamline
   VolumeModelTrackQuilt
   VolumeModelSample
   VolumeModelReorient
   VolumeModelFeature
   VolumeModelSynth
   VolumeVoxelMathScalar
   VolumeModelError
   VolumeNoddiTransform
   VolumeSetSampling

VolumeNoddiAbtin

Name:

 VolumeNoddiAbtin

Description:

 Extract ABTIN (ABsolute TIssue density from NODDI) parameters from a noddi
 volume.  Port from: https://github.com/sepehrband/ABTIN/blob/master/ABTIN.m

Required Input Arguments:

 --input <Volume>
   input noddi volume

Optional Input Arguments:

 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --alpha <double>
   the alpha parameter (see theory section of paper) (Default: 25.0)
 --gratio <double>
   the alpha parameter (see theory section of paper) (Default: 0.7)

Required Output Arguments:

 --outputMylDen <Volume>
   output myelin density volume
 --outputCSFDen <Volume>
   output CSF density volume
 --outputFibDen <Volume>
   output fiber density volume
 --outputCelDen <Volume>
   output cellular density volume

Author:

 Ryan Cabeen

Citation:

 Sepehrband, F., Clark, K. A., Ullmann, J. F.P., Kurniawan, N. D., Leanage,
 G., Reutens, D. C. and Yang, Z. (2015), Brain tissue compartment density
 estimated using diffusion-weighted MRI yields tissue parameters consistent
 with histology. Hum. Brain Mapp.. doi: 10.1002/hbm.22872 Link:
 http://onlinelibrary.wiley.com/doi/10.1002/hbm.22872/abstract

VolumeNoddiBlendExperiment

Name:

 VolumeNoddiBlendExperiment

Description:

 run a noddi blending experiment

Required Input Arguments:

 --gradients <Gradients>
   specify gradientss

Optional Parameter Arguments:

 --size <Integer>
   specify a size (Default: 21)
 --abase <Double>
   specify a noddi parameter (Default: 1)
 --bbase <Double>
   specify a noddi parameter (Default: 1)
 --aicvf <Double>
   specify a noddi parameter (Default: 0.70)
 --bicvf <Double>
   specify a noddi parameter (Default: 0.70)
 --aisovf <Double>
   specify a noddi parameter (Default: 0.01)
 --bisovf <Double>
   specify a noddi parameter (Default: 0.01)
 --aod <Double>
   specify a noddi parameter (Default: 0.2)
 --bod <Double>
   specify a noddi parameter (Default: 0.2)
 --angle <Double>
   specify an angle between models in degrees (Default: 90)

Required Output Arguments:

 --output <Directory>
   specify an output directory

Author:

 Ryan Cabeen

VolumeNoddiFit

Name:

 VolumeNoddiFit

Description:

 Fit a noddi volume

Required Input Arguments:

 --input <Volume>
   input diffusion-weighted MR volume
 --gradients <Gradients>
   the gradients

Optional Input Arguments:

 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --method <String>
   the method for fitting (Grid or Simplex) (Default: Grid)
 --cost <CostType>
   specify a cost function for non-linear fitting (Options: SE, MSE, RMSE,
   NRMSE, CHISQ, RLL) (Default: SE)
 --dpar <Double>
   the parallel diffusivity (change for ex vivo) (Default: 0.0017)
 --diso <Double>
   the isotropic diffusivity (change for ex vivo) (Default: 0.003)
 --dot
   include a dot compartment (set for ex vivo)
 --shells <String>
   specify a subset of gradient shells to include (comma-separated list of
   b-values)
 --which <String>
   specify a subset of gradients to include (comma-separated list of indices
   starting from zero)
 --exclude <String>
   specify a subset of gradients to exclude (comma-separated list of indices
   starting from zero)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   output noddi volume (name output like *.noddi and an directory of volumes
   will be created)

Author:

 Ryan Cabeen

VolumeNoddiFitAMICO

Usage: qit VolumeNoddiFitAMICO [opts]

 fit a NODDI volume with AMICO (installed from

https://github.com/daducci/AMICO)

Options:

 -h, --help            show this help message and exit
 --input=<file>        specify an input DWI (required)
 --gradients=<file>    specify the input gradients (required)
 --mask=<file>         specify a mask (required)
 --output=<dir>        specify an output NODDI directory (required)
 --shells=<a,b,c,...>  specify a subset of gradient shells (comma-separated)
 --which=<a,b,c,...>   specify a subset of gradients to use (comma-separated)
 --exclude=<a,b,c,...>
                       specify a subset of gradients to exclude (comma-
                       separated)
 --dpar=<float>        specify parallel diffusivity parameter (default is
                       1.7e-3)
 --diso=<float>        specify isotropic diffusivity parameter (default is
                       3.0e-3)
 --exvivo              include a dot compartment to support ex-vivo data
 --noflip              do not flip gradients in x
 --save                save the temporary files
 --clobber             clobber existing output

VolumeNoddiFitMatlab

Usage: qit VolumeNoddiFitMatlab [opts]

 fit a noddi model volume using the package at

http://mig.cs.ucl.ac.uk/index.php?n=Tutorial.NODDImatlab. this requires scans with b=0.

Options:

 -h, --help            show this help message and exit
 --input=<file>        specify an input DWI (required)
 --gradients=<file>    specify the input gradients (required)
 --mask=<file>         specify a mask (required)
 --output=<fn>         specify an output noddi volume (required)
 --shells=<a,b,c,...>  specify a subset of gradient shells (comma-separated)
 --which=<a,b,c,...>   specify a subset of gradients to use (comma-separated)
 --exclude=<a,b,c,...>
                       specify a subset of gradients to exclude (comma-
                       separated)
 --exvivo              use the model for ex-vivo (include an isotropic dot)
 --noflip              do not flip gradients in x
 --save                save the temporary files
 --clobber             clobber existing output

VolumeNoddiFuse

Name:

 VolumeNoddiFuse

Description:

 fuse a collection of noddi volumes

Required Input Arguments:

 --input <Volume(s)>
   specify the input noddi volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Optional Parameter Arguments:

 --pattern <String(s)>
   specify a list of names that will be substituted with input %s
 --estimation <String>
   specify a type of estimation (Default: Component)
 --fractions
   use volume fractions in estimation

Required Output Arguments:

 --output <Volume>
   specify the output noddi volume

Author:

 Ryan Cabeen

VolumeNoddiSmooth

Name:

 VolumeNoddiSmooth

Description:

 Smooth a noddi volume

Required Input Arguments:

 --input <Volume>
   the input Noddi volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --hdir <Double>
   the directionally adaptive bandwidth (only used with adaptive flag)
 --hsig <Double>
   the baseline signal adaptive bandwidth
 --estimation <String>
   specify an estimation method (Default: Scatter)

Required Output Arguments:

 --output <Volume>
   the output noddi volume

Author:

 Ryan Cabeen

VolumeNoddiTransform

Name:

 VolumeNoddiTransform

Description:

 Transform a noddi volume

Required Input Arguments:

 --input <Volume>
   the input noddi volume

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)
 --mask <Mask>
   input mask
 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --reorient <ReorientationType>
   specify a reorient method (Options: FiniteStrain, Jacobian) (Default:
   Jacobian)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --estimation <String>
   specify an estimation method (Default: Component)

Required Output Arguments:

 --output <Volume>
   the output transformed noddi volume

Author:

 Ryan Cabeen

VolumeNoddiZoom

Name:

 VolumeNoddiZoom

Description:

 Zoom a noddi volume

Required Input Arguments:

 --input <Volume>
   the input noddi volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --factor <double>
   a zooming factor (Default: 2.0)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional kernel bandwidth in mm (Default: 2.0)
 --hval <Double>
   the data kernel bandwidth
 --hsig <Double>
   the signal kernel bandwidth
 --estimation <String>
   specify an estimation method (Default: Scatter)

Required Output Arguments:

 --output <Volume>
   the output noddi volume

Author:

 Ryan Cabeen

VolumeNoise

Name:

 VolumeNoise

Description:

 Add synthetic noise to a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --sigma <double>
   noise level (Default: 1.0)
 --rician
   use rician distributed noise

Required Output Arguments:

 --output <Volume>
   output mask

Author:

 Ryan Cabeen

VolumeNormalize

Name:

 VolumeNormalize

Description:

 Normalize the values of a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --type <String>
   type of normalization (Unit, UnitMax, UnitMeanGaussian, UnitMeanFraction,
   UnitMaxFraction) (Default: UnitMax)
 --fraction <double>
   a fraction for normalization (only applies to some types of normalization)
   (Default: 0.5)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeOdfFeature

Name:

 VolumeOdfFeature

Description:

 Estimate spherical harmonics representing the ODF.  SUpported features
 include: generalized fractional anisotropy (GFA) and normalized entropy (NE)

Required Input Arguments:

 --input <Volume>
   the input ODF volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --name <String>
   the name of the feature (GFA, NE) (Default: GFA)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output spharm volume

Author:

 Ryan Cabeen

VolumeOdfPeaks

Name:

 VolumeOdfPeaks

Description:

 Extract the peaks from an odf volume.  This finds the average direction of
 local maxima clustered by hierarchical clustering.  The output fibers will
 encode the peak ODF value in place of volume fraction.

Required Input Arguments:

 --input <Volume>
   the input ODF volume
 --dirs <Vects>
   the odf directions

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --comps <Integer>
   the maximum number of comps (Default: 3)
 --gfa
   scale peak values by generalized fractional anisotropy after extraction
 --thresh <Double>
   the minimum peak threshold (Default: 0.0)
 --cluster <Double>
   the minimum angle in degrees for hierarchical clustering of local maxima
   (Default: 5.0)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output fibers volume

Author:

 Ryan Cabeen

VolumeOdfResample

Name:

 VolumeOdfResample

Description:

 Resample an ODF using spherical harmonics.  Using a lower maximum order will
 lead to smoother resamplings

Required Input Arguments:

 --input <Volume>
   the input ODF volume
 --dirs <Vects>
   the input odf directions
 --resample <Vects>
   the directions to resample

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --order <Integer>
   the maximum spherical harmonic order used for resampling (Default: 8)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output ODF volume

Author:

 Ryan Cabeen

VolumeOdfSpharm

Name:

 VolumeOdfSpharm

Description:

 Estimate spherical harmonics representing the ODF

Required Input Arguments:

 --input <Volume>
   the input ODF volume
 --dirs <Vects>
   the odf directions

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --order <Integer>
   the maximum spherical harmonic order (Default: 8)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output spharm volume

Author:

 Ryan Cabeen

VolumeOrigin

Name:

 VolumeOrigin

Description:

 set the origin of a volume

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --x <double>
   the origin in x (Default: 0.0)
 --y <double>
   the origin in y (Default: 0.0)
 --z <double>
   the origin in z (Default: 0.0)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumePhantomBox

Name:

 VolumePhantomBox

Description:

 Create a simple box phantom

Optional Parameter Arguments:

 --width <int>
   image width (Default: 100)
 --height <int>
   image height (Default: 100)
 --slices <int>
   image slices (Default: 1)
 --size <double>
   box relative dimensions (Default: 0.5)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumePoseCopy

Name:

 VolumePoseCopy

Description:

 Set the pose (orientation and origin) of a volume to match a reference volume

Required Input Arguments:

 --input <Volume>
   the input volume
 --ref <Volume>
   the reference volume (the pose will be copied from here)

Optional Parameter Arguments:

 --delta
   copy the voxel spacing as well

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumePoseGet

Name:

 VolumePoseGet

Description:

 Get the pose (orientation and origin) of a volume

Required Input Arguments:

 --input <Volume>
   the input volume

Required Output Arguments:

 --output <Affine>
   the output affine xfm

Author:

 Ryan Cabeen

VolumePoseSet

Name:

 VolumePoseSet

Description:

 Set the pose (orientation and origin) of a volume.  By default, the existing
 origin and orientation will be removed

Required Input Arguments:

 --input <Volume>
   the input volume
 --pose <Affine>
   the affine pose (any shear will be removed)

Optional Parameter Arguments:

 --premult
   compose the existing pose with the given one by premultiplying
 --postmult
   compose the existing pose with the given one by post multiplying

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumePrintInfo

Name:

 VolumePrintInfo

Description:

 Print basic information about a volume

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --stats
   print statistics
 --nifti
   print complete nifti header (only relevant if the input is nifti)

Author:

 Ryan Cabeen

VolumeProjection

Name:

 VolumeProjection

Description:

 Compute a projection of an image volume along one axis, for example a minimum
 intensity projection

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --axis <VolumeProjectionAxis>
   the axis for the projection (Options: i, j, k) (Default: k)
 --type <VolumeProjectionType>
   the type of statistic for the projection (Options: Min, Max, Mean, Sum,
   Var, CV, Median, IQR) (Default: Mean)
 --thin <Integer>
   use thin projection, whereby groups of the given number of slices are
   aggregated
 --index <int>
   when collapsing the volume to a single slice, use this image index for the
   position (Default: 0)

Required Output Arguments:

 --output <Volume>
   output image slice

Author:

 Ryan Cabeen

VolumeReduce

Name:

 VolumeReduce

Description:

 Reduce a multi-channel volume to a volume with fewer channels

Required Input Arguments:

 --input <Volume>
   input volume

Optional Parameter Arguments:

 --which <String>
   the list of indices to select (comma separated zero-based indices)
 --exclude <String>
   exclude specific indices (comma separated zero-based indices)
 --mean
   compute the mean volume
 --max
   compute the max volume
 --min
   compute the max volume

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeRegionMinima

Name:

 VolumeRegionMinima

Description:

 Mask a volume

Required Input Arguments:

 --input <Volume>
   input volume
 --regions <Mask>
   a mask encoding regions
--lookup
a table encoding region names Optional Input Arguments: --mask <Mask> a mask restricting which voxels are checked Optional Parameter Arguments: --minimum retain the minimum value --sample retain the sample voxel indices --index <String> specify the lookup index field (Default: index) --name <String> specify the lookup name field (Default: name) --min <String> specify the output field name for the minimum value (Default: min) --i <String> specify the output field name for the sample i index (Default: i) --j <String> specify the output field name for the sample j index (Default: j) --k <String> specify the output field name for the sample k index (Default: k) Required Output Arguments: --output
output table Author: Ryan Cabeen

VolumeRegisterFlirt

Usage: qit VolumeRegisterFlirt [opts]

register volumetric data using FSL

Options:

 -h, --help          show this help message and exit
 --input=<fn>        specify the input
 --ref=<fn>          specify the reference
 --inv-xfm-out=<fn>  write out the inverse transform
 --xfm-out=<fn>      write out the transform
 --cost=<str>        specify the cost function
 --dof=<int>         specify the degrees of freedom

VolumeRender

Name:

 VolumeRender

Description:

 Render a volume slice based on a colormap

Optional Input Arguments:

 --background <Volume>
   input background
 --foreground <Volume>
   input foreground colored using a scalar colormap
 --labels <Mask>
   input labels colored using a discrete colormap
 --fgmask <Mask>
   input foreground mask
 --bgmask <Mask>
   input background mask

Optional Parameter Arguments:

 --range <String>
   input slice range, e.g. :,:,80 (Default: all)
 --bgmap <String>
   background colormap (Default: grayscale)
 --bglow <String>
   background lower bound (supports statistics like min, max, etc) (Default:
   0)
 --bghigh <String>
   background upper bound (supports statistics like min, max, etc) (Default:
   1)
 --fgmap <String>
   scalar colormap for coloring the volume (Default: grayscale)
 --fglow <String>
   scalar lower bound (supports statistics like min, max, etc) (Default: 0)
 --fghigh <String>
   scalar upper bound (supports statistics like min, max, etc) (Default: 1)
 --fgrlow <String>
   scalar lower bound for range (0 to 1) (Default: 0)
 --fgrhigh <String>
   scalar upper bound for range (0 to 1) (Default: 1)
 --discrete <String>
   discrete colormap for coloring the label volume (Default: White)
 --invert
   invert colormap
 --wash <double>
   wash out colors (Default: 0.0)
 --alpha <double>
   blending of background with foreground (Default: 1.0)
 --label <String>
   a label for the colormap (Default: attribute)

Optional Output Arguments:

 --output <Volume>
   output RGB volume rendering
 --colormap <Volume>
   output RGB colormap rendering

Author:

 Ryan Cabeen

VolumeResample

Name:

 VolumeResample

Description:

 Resample a volume with a different voxel size

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --dx <double>
   the voxel size in x (Default: 1.0)
 --dy <double>
   the voxel size in y (Default: 1.0)
 --dz <double>
   the voxel size in z (Default: 1.0)
 --interp <InterpolationType>
   image interpolation method (Options: Nearest, Trilinear, Tricubic,
   Gaussian, GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumeReslice

Name:

 VolumeReslice

Description:

 Reslice a volume.  You must specify the new slicing by either a solids object
 containing a plane or by a collection of vects.

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --vects <Vects>
   input vects (should roughly lie on a straight line)
 --plane <Solids>
   input solids (should contain a plane)
 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --delta <Double>
   the voxel spacing (by default it detects it from the input)
 --interp <InterpolationType>
   image interpolation method (Options: Nearest, Trilinear, Tricubic,
   Gaussian, GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeSampleLine

Name:

 VolumeSampleLine

Description:

 Sample a volume along a polyline.  The results are stored in table along with
 the world coordinates and position along the segment

Required Input Arguments:

 --input <Volume>
   input volume
 --vects <Vects>
   input vects (two points in a vects object)

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --num <int>
   the number of samples (Default: 5)
 --interp <InterpolationType>
   image interpolation method (Options: Nearest, Trilinear, Tricubic,
   Gaussian, GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)
 --value <String>
   the name of the volume value field (Default: value)
 --dims <String>
   a which of dimensions to use
 --vector
   include vector values
 --vx <String>
   the field for the x coordinate (Default: x)
 --vy <String>
   the field for the y coordinate (Default: y)
 --vz <String>
   the field for the z coordinate (Default: z)
 --pos <String>
   the position along the line segment in mm (Default: pos)
 --idx <String>
   the index along the line segment (Default: idx)

Required Output Arguments:

--output
output table Author: Ryan Cabeen

VolumeSegmentCluster

Name:

 VolumeSegmentCluster

Description:

 Segment a volume by clustering intensities (with k-means, dp-means, or
 Gaussian mixtures)

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --iters <int>
   a maximum number of iterations (Default: 10)
 --num <int>
   the number classes (inital guess in the case of dp-means) (Default: 3)
 --restarts <int>
   the number of restarts (Default: 1)
 --thresh <double>
   the convergence threshold (Default: 0.001)
 --lambda <Double>
   a threshold for detecting the number of clusters in the DP-means algorithm
 --gmm
   use a Gaussian mixture model for clustering (initialized by k-means)
 --cov <String>
   specify a covariance type (spherical, diagonal, full) (Default: spherical)
 --reg <double>
   a regularization parameter added to the covariance (Default: 0.01)
 --smooth
   use spatial smoothing
 --window <int>
   specify a spatial smoothing window (Default: 1)

Optional Output Arguments:

 --labels <Mask>
   none
 --membership <Volume>
   none
 --model <Dataset>
   none

Author:

 Ryan Cabeen

VolumeSegmentGraph

Name:

 VolumeSegmentGraph

Description:

 Segment a volume using graph based segmentation

Required Input Arguments:

 --input <Volume>
   the input tensor volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --min <Integer>
   a minima region size (Default: 10)
 --threshold <Double>
   a threshold for grouping (Default: 1.0)

Required Output Arguments:

 --output <Mask>
   the output segmentation mask

Author:

 Ryan Cabeen

Citation:

 Felzenszwalb, P. F., & Huttenlocher, D. P. (2004). Efficient graph-based
 image segmentation. International journal of computer vision, 59(2), 167-181.
 Chicago

VolumeSegmentRegionGrowing

Name:

 VolumeSegmentRegionGrowing

Description:

 Segment a volume using a statistical region-growing technique

Required Input Arguments:

 --input <Volume>
   the input volume
 --seeds <Mask>
   the input mask

Optional Parameter Arguments:

 --thresh <Double>
   the stopping threshold (Default: 1.0)
 --maxiter <int>
   the maxima number of iterations (Default: 10000)
 --maxsize <double>
   the maxima region volume (Default: 1.7976931348623157E308)
 --full
   use a full 27-voxel neighborhood (default is 6-voxel)
 --recurse
   use the output as input

Required Output Arguments:

 --output <Mask>
   the output segmentation

Author:

 Ryan Cabeen

Citation:

 Adams, R., & Bischof, L. (1994). Seeded region growing. IEEE Transactions on
 pattern analysis and machine intelligence, 16(6), 641-647.

VolumeSegmentSuperKMeans

Name:

 VolumeSegmentSuperKMeans

Description:

 Segment supervoxels from a volume using k-means.  Voxels are clustered based
 on position and intensity

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --iters <int>
   a maxima number of iterations (Default: 10)
 --num <int>
   the number regions (Default: 100)
 --scale <double>
   the scale for combining intensities with voxel positions (Default: 1.0)

Required Output Arguments:

 --output <Mask>
   none

Author:

 Ryan Cabeen

VolumeSegmentSuperSLIC

Name:

 VolumeSegmentSuperSLIC

Description:

 Segment a volume to obtain SLIC supervoxels

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --iters <int>
   a maximum number of iterations (Default: 500)
 --error <double>
   the convergence criteria (Default: 0.001)
 --size <double>
   the average size (along each dimension) for the supervoxels (Default: 20.0)
 --scale <double>
   the scale for intensities (Default: 1.0)
 --merge <double>
   a threshold region volume for merging (Default: 10.0)
 --group <Double>
   a threshold gradient magnitude for grouping

Required Output Arguments:

 --output <Mask>
   none

Author:

 Ryan Cabeen

Citation:

 Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua,
 and Sabine Susstrunk, SLIC Superpixels, EPFL Technical Report 149300, June
 2010.

VolumeSetSampling

Name:

 VolumeSetSampling

Description:

 Set the origin of a volume

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --starti <Double>
   the origin in i
 --startj <Double>
   the origin in j
 --startk <Double>
   the origin in k
 --deltai <Double>
   the voxel spacing in i
 --deltaj <Double>
   the voxel spacing in j
 --deltak <Double>
   the voxel spacing in k

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumeSetTable

Name:

 VolumeSetTable

Description:

 Create a table listing regions of a mask

Required Input Arguments:

 --reference <Volume>
   input volume
--table
input table Optional Parameter Arguments: --dim <int> the channel (Default: 0) --index <String> the index field name (Default: index) --value <String> a field to set (Default: value) --background <double> a background value (Default: 0.0) --missing <Double> a missing value Required Output Arguments: --output <Volume> output volume Author: Ryan Cabeen

VolumeSkeletonize

Name:

 VolumeSkeletonize

Description:

 Extract a skeleton from the local maxima and ridges of a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --threshold <Double>
   exclude voxels with an input intensity below this value

Required Output Arguments:

 --output <Mask>
   output skeleton

Author:

 Ryan Cabeen

VolumeSlice

Name:

 VolumeSlice

Description:

 Threshold a volume to make a mask

Required Input Arguments:

 --input <Volume>
   input volume

Optional Parameter Arguments:

 --slice <int>
   a slice number (Default: 0)
 --dim <String>
   a slice channel (x, y, or z) (Default: z)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeSliceMesh

Name:

 VolumeSliceMesh

Description:

 Create a mesh from image slices

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   input mask

Optional Parameter Arguments:

 --attribute <String>
   specify a name for the attribute (Default: data)
 --range <String>
   specify a range of slices to extract (or a specific slice) (Default:
   start:25:end)
 --axis <VolumeSliceMeshAxis>
   the slice axis (Options: i, j, k) (Default: k)
 --nobg
   remove background voxels
 --thresh <double>
   specify a threshold for background removal (Default: 1.0E-6)
 --color
   add vertex colors
 --normalize
   use min/max normalization

Required Output Arguments:

 --output <Mesh>
   output mesh

Author:

 Ryan Cabeen

VolumeSliceMesh$1

 No module named VolumeSliceMesh$1 was found!
 Maybe you are looking for one of these?
   VolumeSliceMesh
   VolumeSlice
   VolumeFibersFit
   VolumeOdfPeaks
   VolumeThreshold
   VolumeFibersZoom
   VolumeTile
   VolumePoseGet
   VolumeNoise
   VolumeSurfacePlot

VolumeSpharmFitMrtrix

Usage: qit VolumeSpharmFitMrtrix [opts]

 fit a spherical harmonics volume with mrtrix

Options:

 -h, --help            show this help message and exit
 --input=<file>        specify an input DWI (required)
 --gradients=<file>    specify the input gradients (required)
 --mask=<file>         specify a mask (required)
 --output=<fn>         specify an output spharm volume (required)
 --shells=<a,b,c,...>  specify a subset of gradient shells (comma-separated)
 --which=<a,b,c,...>   specify a subset of gradients to use (comma-separated)
 --exclude=<a,b,c,...>
                       specify a subset of gradients to exlcude (comma-
                       separated)
 --response=<name>     specify a response estimation method
 --fod=<name>          specify an fod estimation method (old indicates an
                       older version of mrtrix that did not support this
                       option)
 --noflip              do not flip gradients in x
 --save                save the temporary files
 --clobber             clobber existing output

VolumeSpharmODF

Name:

 VolumeSpharmODF

Description:

 Sample an orientation distribution function (ODF) from a spharm volume.

Required Input Arguments:

 --input <Volume>
   the input spharm volume
 --dirs <Vects>
   the sphere directions

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output odf volume

Author:

 Ryan Cabeen, Dogu Baran Aydogan

VolumeSpharmPeaks

Name:

 VolumeSpharmPeaks

Description:

 Extract the peaks from a spherical harmonic volume.  This finds the average
 direction of local maxima clustered by hierarchical clustering.  The output
 fibers will encode the peak q-value in place of volume fraction.

Required Input Arguments:

 --input <Volume>
   the input spharm volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --comps <Integer>
   the maximum number of comps (Default: 3)
 --thresh <Double>
   the minimum peak threshold (Default: 0.1)
 --detail <Integer>
   the level of detail for spherical harmonic sampling (Default: 20)
 --cluster <Double>
   the minimum angle in degrees for hierarchical clustering of local maxima
   (Default: 5.0)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output fibers volume

Author:

 Ryan Cabeen

VolumeSpharmTrackMRtrix

Name:

 VolumeSpharmTrackMRtrix

Description:

 Perform probabilistic tractography from a spharm volume using an
 implementation of the iFOD1 algorithm from MRtrix.

Required Input Arguments:

 --input <Volume>
   the input spharm volume

Optional Input Arguments:

 --seedVects <Vects>
   seed from vects
 --seedMask <Mask>
   a seed mask (one seed per voxel is initiated from this)
 --seedSolids <Solids>
   seed from solids (one seed per object is initiated from this)
 --includeMask <Mask>
   an include mask (see --and flag)
 --includeSolids <Solids>
   an include solids object (see --and flag)
 --excludeMask <Mask>
   an exclude mask (curves are removed if they touch this mask)
 --stopMask <Mask>
   a stop mask (tracking terminates when reaching this mask)
 --stopSolids <Solids>
   a stop solids object (tracking terminates when reaching any solid)
 --trackMask <Mask>
   a tracking mask (tracking is stopped if a curve exits this mask)
 --trackSolids <Solids>
   a tracking solids (tracking is stopped if a curve exits solids)

Optional Parameter Arguments:

 --samples <Integer>
   the number of samples per seed object (e.g. voxels, spheres, boxes, etc)
   (Default: 1)
 --angle <Double>
   the angle stopping criteria (will be normalized by step size) (Default:
   45.0)
 --step <Double>
   the step size for tracking (Default: 1.0)
 --min <double>
   a minimum value for tracking (Default: 0.1)
 --trials <Integer>
   the maximum number of trials for rejection sampling (Default: 50)
 --cone <Integer>
   the number of samples for fod maxima detections (Default: 12)
 --rk
   use fourth-order Runge-Kutta integration (default is Euler)
 --length <Double>
   the minimum streamline length (Default: 0.0)
 --limit <Integer>
   a maximum number of seeds (Default: 2000000)
 --or
   take the logical OR when multiple include objects are present (default is
   AND)
 --interp <InterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Tricubic, Gaussian,
   GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)
 --mixing <Double>
   the mixing weight for orientation updates (0 to 1) (Default: 1.0)
 --arclen <Double>
   an arclength containment threshold (Default: 0.8)
 --reach <Double>
   only allow tracking to travel a given reach distance from the seed
 --endpoints
   require curve endpoints to lie inside masks
 --empty
   include empty curves for seeds that don't track
 --mono
   use monodirectional seeding (default is bidirectional)
 --threads <int>
   the number of threads (Default: 3)

Required Output Arguments:

 --output <Curves>
   the output tractography curves

Author:

 Ryan Cabeen, Dogu Baran Aydogan

Citation:

 Tournier, J., Fernando Calamante, and Alan Connelly. "MRtrix: diffusion
 tractography in crossing fiber regions." International Journal of Imaging
 Systems and Technology 22.1 (2012): 53-66.

VolumeSplit

Name:

 VolumeSplit

Description:

 Split a multi-channel volume into multiple seperate volumes

Required Input Arguments:

 --input <File>
   specify an input multi-channel volume

Optional Parameter Arguments:

 --which <Integers(s)>
   specify a subset of channels to extract

Required Output Arguments:

 --output <Pattern>
   specify the output filename pattern with %d (will correspond to the channel
   number)

Author:

 Ryan Cabeen

VolumeStandardize

Name:

 VolumeStandardize

Description:

 Standardize the orientation of a volume (no rotation and zero origin).  The
 original pose can be saved to xfm.

Required Input Arguments:

 --input <Volume>
   input Volume

Optional Output Arguments:

 --output <Volume>
   output Volume
 --xfm <Affine>
   output affine
 --invxfm <Affine>
   output inverse affine

Author:

 Ryan Cabeen

VolumeSubset

Name:

 VolumeSubset

Description:

 Which the intensities of a volume

Required Input Arguments:

 --input <Volume>
   input volume

Required Parameter Arguments:

 --which <String>
   the list of indices to select

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeSurfacePlot

Name:

 VolumeSurfacePlot

Description:

 Plot data from a planar image

Required Input Arguments:

 --input <Volume>
   input

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --dimension <int>
   the channel (Default: 0)
 --sx <double>
   the scale in x (Default: 1.0)
 --sy <double>
   the scale in y (Default: 1.0)
 --sz <double>
   the scale in z (Default: 1.0)

Required Output Arguments:

 --output <Mesh>
   output

Author:

 Ryan Cabeen

VolumeTable

Name:

 VolumeTable

Description:

 Record voxel values in a table

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   a mask
--lookup
a lookup table for matching names to mask labels Optional Parameter Arguments: --value <String> value (Default: value) --multiple use multiple mask labels --lookupNameField <String> specify the lookup name field (Default: name) --lookupIndexField <String> specify the output voxel field name (Default: voxel) --range <String> a mask specification --dims <String> a which of dimensions to use --vector include vector values --vi <String> the field for the voxel i coordinate --vj <String> the field for the voxel j coordinate --vk <String> the field for the voxel k coordinate --voxel <String> the field for the voxel voxel (Default: voxel) Required Output Arguments: --output
output table Author: Ryan Cabeen

VolumeTensorFit

Name:

 VolumeTensorFit

Description:

 Fit a tensor volume to a diffusion-weighted MRI.

Required Input Arguments:

 --input <Volume>
   input diffusion-weighted MR volume
 --gradients <Gradients>
   the gradients

Optional Input Arguments:

 --mask <Mask>
   the mask

Optional Parameter Arguments:

 --method <TensorFitType>
   specify an estimation method (Options: LLS, WLLS, NLLS, FWLLS, FWWLLS,
   FWNLLS) (Default: LLS)
 --cost <CostType>
   specify a cost function for non-linear fitting (Options: SE, MSE, RMSE,
   NRMSE, CHISQ, RLL) (Default: SE)
 --shells <String>
   specify a subset of gradient shells to include (comma-separated list of
   b-values)
 --which <String>
   specify a subset of gradients to include (comma-separated list of indices
   starting from zero)
 --exclude <String>
   specify a subset of gradients to exclude (comma-separated list of indices
   starting from zero)
 --baseline
   estimate the baseline value separately from tensor parameter estimation
   (only for LLS)
 --threads <int>
   the number of threads to use (Default: 1)

Required Output Arguments:

 --output <Volume>
   output tensor volume (name output like *.dti and an directory of volumes
   will be created)

Author:

 Ryan Cabeen

VolumeTensorFuse

Name:

 VolumeTensorFuse

Description:

 fuse a collection of tensor volumes

Required Input Arguments:

 --input <Volume(s)>
   specify the input tensor volumes

Optional Input Arguments:

 --mask <Mask>
   specify a mask

Optional Parameter Arguments:

 --pattern <String(s)>
   specify a list of names that will be substituted with input %s
 --log
   use log-euclidean estimation

Required Output Arguments:

 --output <Volume>
   specify the output tensor volume

Author:

 Ryan Cabeen

VolumeTensorNoise

Name:

 VolumeTensorNoise

Description:

 Add noise to a tensor volume

Required Input Arguments:

 --input <Volume>
   input tensor volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --sigma <Double>
   the sigma of the noise

Required Output Arguments:

 --output <Volume>
   output tensor volume

Author:

 Ryan Cabeen

VolumeTensorOdf

Name:

 VolumeTensorOdf

Description:

 Sample an orientation distribution function (ODF) from a tensor volume.

Required Input Arguments:

 --input <Volume>
   the input tensor volume
 --dirs <Vects>
   the sphere directions

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --alpha <Double>
   the alpha power value (Default: 1.0)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   the output odf volume

Author:

 Ryan Cabeen

VolumeTensorRegister

Usage: qit TensorVolumeRegister [opts] in_dir target_dir out_dir

 Register diffusion tensor images with DTI-TK.  Note: diffusivities are

assumed to be 10^-3 mm^2 s^-1. Correction factors must be set when this is not the case. The default scaling is 1000 to support FSL style units.

Options:

 -h, --help            show this help message and exit
 --mask=<fn>           specify a target volume mask
 --scale=<val>         specify an input diffusivity scaling
 --target-scale=<val>  specify a target diffusivity scaling
 --outlier=<val>       specify a threshold for outlier detection
 --intermediate        keep intermediate files
 --thresh=<thresh>     the fa threshold for tracking

VolumeTensorRegisterDtitk

Usage: qit VolumeTensorRegisterDtitk [opts]

 Deformable registration of  diffusion tensor images with DTI-TK.  Note:

diffusivities are assumed to be mm^2 s^-1, so you might have to adjust them if your target has different units from the input.

Options:

 -h, --help            show this help message and exit
 --input=<dti>         specify an input DTI volume (directory or image)
 --target=<dti>        specify a target DTI volume (directory or image)
 --mask=<fn>           specify a target volume mask
 --scale=<val>         specify an input diffusivity scaling
 --target-scale=<val>  specify a target diffusivity scaling
 --outlier=<val>       specify a threshold for outlier detection
 --intermediate=<dir>  save intermediate files to the given directory
 --output-xfm=<fn>     the output transform
 --output-invxfm=<fn>  the output inverse transform

VolumeTensorSegmentGraph

Name:

 VolumeTensorSegmentGraph

Description:

 Tensor volume graph-based segmentation based on principal direction

Required Input Arguments:

 --input <Volume>
   the input tensor volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --line
   use a line metric
 --log
   use a log Euclidean metric
 --threshold <Double>
   a threshold for grouping (Default: 1.0)

Required Output Arguments:

 --output <Mask>
   the output segmentation mask

Author:

 Ryan Cabeen

VolumeTensorSegmentSuper

Name:

 VolumeTensorSegmentSuper

Description:

 Segment supervoxels from a tensor volume

Required Input Arguments:

 --input <Volume>
   the input tensor volume
 --mask <Mask>
   a mask

Optional Input Arguments:

 --weights <Volume>
   a weight volume

Optional Parameter Arguments:

 --size <Integer>
   a threshold size (any region smaller than this will be removed)
 --iters <Integer>
   the number of iterations (Default: 10)
 --restarts <Integer>
   the number of restarts
 --num <Integer>
   the number of clusters (the initial number if dp-means is used) (Default:
   100)
 --alpha <Double>
   the alpha parameter for spatial extent (Default: 1.0)
 --beta <Double>
   the beta parameter for angular extent (Default: 15.0)
 --lambda <Double>
   the lambda parameter for region size (for dp-means clustering)

Required Output Arguments:

 --output <Mask>
   the output segmentation mask

Author:

 Ryan Cabeen

VolumeTensorSmooth

Name:

 VolumeTensorSmooth

Description:

 Smooth a tensor volume

Required Input Arguments:

 --input <Volume>
   the input tensor volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --hdir <Double>
   the tensor adaptive bandwidth
 --hsig <Double>
   the baseline signal adaptive bandwidth
 --log
   use log-euclidean processing
 --frac <Double>
   exclude voxels below a give FA (Default: 0.0)

Required Output Arguments:

 --output <Volume>
   the output tensor volume

Author:

 Ryan Cabeen

VolumeTensorThreshold

Name:

 VolumeTensorThreshold

Description:

 Create a mask from a tensor volume using a complex expression

Required Input Arguments:

 --input <Volume>
   the input tensor volume

Optional Input Arguments:

 --mask <Mask>
   mask

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: FA > 0.15 && MD < 0.001 && MD >
   0.0001)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

VolumeTensorTransform

Name:

 VolumeTensorTransform

Description:

 Spatially transform a tensor volume

Required Input Arguments:

 --input <Volume>
   the input tensor volume

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)
 --mask <Mask>
   input mask
 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --reorient <ReorientationType>
   specify a reorient method (fs or jac) (Options: FiniteStrain, Jacobian)
   (Default: Jacobian)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 1.0)
 --log
   use log estimation

Required Output Arguments:

 --output <Volume>
   the output transformed tensor volume

Author:

 Ryan Cabeen

VolumeTensorTransformDtitk

Usage: qit TensorVolumeTransform [opts] input xfm target output

 Transform a diffusion tensor volume.

Options:

 -h, --help         show this help message and exit
 --affine           perform affine registration
 --scale=<val>      specify an input diffusivity scaling
 --outlier=<val>    specify a threshold for outlier detection
 --intermediate     keep intermediate files
 --thresh=<thresh>  the fa threshold for tracking

VolumeTensorZoom

Name:

 VolumeTensorZoom

Description:

 Zoom a tensor volume

Required Input Arguments:

 --input <Volume>
   the input tensor volume

Optional Input Arguments:

 --mask <Mask>
   a mask

Optional Parameter Arguments:

 --factor <double>
   a zooming factor (Default: 2.0)
 --interp <KernelInterpolationType>
   the interpolation type (Options: Nearest, Trilinear, Gaussian) (Default:
   Trilinear)
 --log
   use log euclidean estimation
 --support <Integer>
   the filter radius in voxels (Default: 3)
 --hpos <Double>
   the positional bandwidth in mm (Default: 2.0)

Required Output Arguments:

 --output <Volume>
   the output tensor volume

Author:

 Ryan Cabeen

VolumeThreshold

Name:

 VolumeThreshold

Description:

 Threshold a volume to make a mask

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --mask <Mask>
   mask

Optional Parameter Arguments:

 --threshold <double>
   threshold value (Default: 0.5)

Required Output Arguments:

 --output <Mask>
   output mask

Author:

 Ryan Cabeen

VolumeTile

Name:

 VolumeTile

Description:

 Tile a collection of volumes in a single volume

Optional Parameter Arguments:

 --pattern <String>
   the input pattern (should contain ${x} and ${y}) (Default:
   volume.${x}.${y}.nii.gz)
 --xids <String>
   the row identifiers to be substituted (Default: a,b,c)
 --yids <String>
   the column identifiers to be substituted (Default: 1,2,3,4)
 --xbuffer <int>
   a buffer size between tiles (Default: 0)
 --ybuffer <int>
   a buffer size between tiles (Default: 0)
 --orientation <String>
   slice orientation for storing a stack (x, y, or z) (Default: z)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumeTransform

Name:

 VolumeTransform

Description:

 Transform a volume

Required Input Arguments:

 --input <Volume>
   input volume

Optional Input Arguments:

 --refvolume <Volume>
   input reference volume (exclusive with refmask)
 --refmask <Mask>
   input reference mask (exclusive with refvolume)
 --mask <Mask>
   input mask
 --affine <Affine>
   apply an affine xfm
 --invaffine <Affine>
   apply an inverse affine xfm
 --deform <Deformation>
   apply a deformation xfm

Optional Parameter Arguments:

 --interp <InterpolationType>
   image interpolation method (Options: Nearest, Trilinear, Tricubic,
   Gaussian, GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)
 --reorient
   reorient vector image data
 --reoriention <ReorientationType>
   specify a reorient method (fs or jac) (Options: FiniteStrain, Jacobian)
   (Default: Jacobian)
 --threads <Integer>
   the number of threads in the pool (Default: 1)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeVoxelMathScalar

Name:

 VolumeVoxelMathScalar

Description:

 Evaluate an expression at each voxel of volume data

Required Input Arguments:

 --x <Volume>
   the x input volume

Optional Input Arguments:

 --y <Volume>
   the y input volume
 --z <Volume>
   the z input volume
 --w <Volume>
   the w input volume
 --mask <Mask>
   mask

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: x > 0.5)

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeVoxelMathVect

Name:

 VolumeVoxelMathVect

Description:

 Evaluate an expression at each voxel of volume data

Required Input Arguments:

 --x <Volume>
   the x input volume

Optional Input Arguments:

 --y <Volume>
   the y input volume
 --z <Volume>
   the z input volume
 --w <Volume>
   the w input volume
 --mask <Mask>
   mask

Optional Parameter Arguments:

 --expression <String>
   the expression to evaluate (Default: mean(x))

Required Output Arguments:

 --output <Volume>
   output volume

Author:

 Ryan Cabeen

VolumeZoom

Name:

 VolumeZoom

Description:

 Zoom a volume.  Note: be careful using this for downsampling, as it does not
 apply an anti-aliasing prefilter.

Required Input Arguments:

 --input <Volume>
   the input volume

Optional Parameter Arguments:

 --factor <Double>
   an isotropic scaling factor
 --fi <Double>
   a scaling factor in i
 --fj <Double>
   a scaling factor in j
 --fk <Double>
   a scaling factor in k
 --interp <InterpolationType>
   an interpolation type (Options: Nearest, Trilinear, Tricubic, Gaussian,
   GaussianLocalLinear, GaussianLocalQuadratic) (Default: Trilinear)
 --threads <Integer>
   the number of threads in the pool (Default: 3)

Required Output Arguments:

 --output <Volume>
   the output volume

Author:

 Ryan Cabeen

VolumesTable

Name:

 VolumesTable

Description:

 create a table from one or multiple volumes

Required Input Arguments:

 --input <String=Volume(s)>
   specify the input volumes (field=file field2=file2 ...)

Optional Input Arguments:

 --mask <Mask>
   specify a mask
--lookup
use a lookup to map mask labels to names Optional Parameter Arguments: --pattern <String(s)> specify a list of names that will be substituted with input %s --multiple use multiple mask labels --lookupNameField <String> specify a name field in the lookup table (Default: name) --lookupIndexField <String> specify an voxel field in the lookup table (Default: index) --vi <String> specify a voxel i voxel name --vj <String> specify a voxel j voxel name --vk <String> specify a voxel k voxel name --voxel <String> specify a voxel voxel field name (Default: voxel) Required Output Arguments: --output
specify the output table Author: Ryan Cabeen