EXTRACT_Profile

Extract fiber tract statistics from images

Command:

dmrifiberprofile

Module version:

0.1

Module type:

fiberprofile

Attributes:

utility

Source:

dtiplayground/dmri/fiberprofile/modules/EXTRACT_Profile

Protocol options

atlas

Directory containing set of fiber tracts in the atlas to be analyzed

Type:

dirpath-remote

Default:

not set

tracts

Selected set of tracts to use. Must uniquely map to a VTK fiber file in the atlas location. Empty - all the tracts (.vtk) of the atlas folder.

Type:

filepath-remote-mult

Default:

not set

inputIsDTI

Input image is a DTI (column ‘Original DTI Image’). The tensors are interpolated along the fibers and FA, MD, AD, RD are computed from them; <prefix>FA, <prefix>MD, <prefix>AD, <prefix>RD are computed from the tensors of the column ‘<prefix> DTI Image’ if the column map has that key (e.g. FWFA from ‘FW DTI Image’). Other properties, or all properties if this is off, are sampled from their own scalar image column. A property whose image cell is empty for a subject is not profiled for that subject.

Type:

boolean

Default:

true

tensorInterpolation

Interpolation of the DTI along the fibers (only if the input is a DTI)

Type:

list

Default:

logEuclidean

Choices:

  • logEuclidean – Linear interpolation of the matrix logarithms of the tensors (no swelling effect). Voxels without a positive definite tensor are left out.

  • linear – Linear interpolation of the tensor components (as fiberprocess)

propertiesToProfile

List of selected properties to profile along tracts

Type:

string

Default:

FA, MD, RD, AD

useDisplacementField

Convert image to atlas space using displacement field. If set to false, the image will not be transformed to atlas space.

Type:

boolean

Default:

true

parameterToColumnHeaderMap

Datasheet column of each parameter: Case ID, Original DTI Image, Deformation Field, ‘<prefix> DTI Image’ (additional tensor images, e.g. FW DTI Image), and the image of each scalar property

Type:

dictionary

Default:

Case ID: id, Original DTI Image: Original DTI image, Deformation Field: Concatenated Deformation field, FA: FA from original, MD: MD from original, AD: AD from original, RD: RD from original

resultCaseColumnwise

In output CSV, store cases as columns instead of rows

Type:

boolean

Default:

true

planeOfOrigin

Determines plane that sets the origin of the profile arc length

Type:

list

Default:

Median

Choices:

  • Median – Origin of profile will be median of tract

  • CoG – Origin of profile will be center of gravity

arcLength

Source of the arc length of the fiber points

Type:

list

Default:

stored

Choices:

  • stored – Use the arc lengths stored in parametrized tracts (point data SamplingDistance2Origin, e.g. written by dmrifiberprofile parametrize-fibers); computed from the plane of origin if the tract has none

  • compute – Always compute the arc lengths from the plane of origin

cleanup

Remove the profiles of each scan (.fvp, per property and tract folders) and fiber files after processing; kept, they are reused by a later run when their settings and input files are unchanged

Type:

list

Default:

noCleanup

Choices:

  • noCleanup – Keep the profile of each scan (.fvp) and fiber files; a later run reuses the profiles whose settings and input files are unchanged

  • duringProcessing – Remove the profiles of each scan (.fvp) and fiber files the moment they’re no longer needed (everything is recomputed by a later run)

  • endOfProcessing – Remove the profiles of each scan (.fvp) and fiber files after processing is complete (everything is recomputed by a later run)

stepSize

Distance (mm) along the tract between profile samples; samples are at multiples of the step size from the plane of origin

Type:

float

Default:

1

supportBandwidth

Standard deviation (mm) of the Gaussian kernel; points within this distance of a sample are averaged

Type:

float

Default:

3

noNaN

Remove fibers with NaN values of the profiled property (for each subject)

Type:

boolean

Default:

false

writeFiberFiles

Write the fibers of each subject with the sampled property values and arc lengths (one VTK file per subject, property and tract, e.g. to view the values along the fibers). Not needed for the profiles; removed by the cleanup like the .fvp profiles

Type:

boolean

Default:

false

mask

Optional mask file to use during profile extraction. Mask has to be defined in atlas space.

Type:

file

Default:

not set

maskThreshold

Fibers whose average mask value along the fiber is below this threshold are removed (only used with a mask)

Type:

float

Default:

0.5