BRAIN_Tractography

Brain tractography (whole/single region) using DIPY library

Command:

dmriprep

Module version:

0.1

Module type:

prep

Attributes:

utility

Notes:

BRAIN_Tractography README

Source:

dtiplayground/dmri/preprocessing/modules/BRAIN_Tractography

Protocol options

whiteMatterMaskThreshold

Manual or Otsu threshold on FA to get a white matter mask of the brain

Type:

list

Default:

manual

Choices:

  • manual – Use manual threshold on FA to create a white matter mask

thresholdLow

Lower value of threshold to apply on FA

Type:

number

Default:

0.4

thresholdUp

Upper value of threshold to apply on FA

Type:

number

Default:

0.98

method

Method used to generate the peaks used to generate the streamlines

Type:

list

Default:

tensor

Choices:

  • csa – Constant Solid Angle method

  • opdt – Orientation Probability Density Transform method

  • tensor – DTI tensor method

shOrder

sh order used for peak generation model

Type:

number

Default:

2

relativePeakThreshold

Only keeps peaks greater than relativePeakThreshold * m where m is the largest peak

Type:

number

Default:

0.9

minPeakSeparationAngle

The minimum distance between directions. If two peaks are too close only the larger of the two is returned. Number between 0 and 90.

Type:

number

Default:

25

stoppingCriterionThreshold

Threshold on FA to stop tracts

Type:

number

Default:

0.3

vtk42

Save output tractogram in VTK format 4.2 (instead of 5.0)

Type:

boolean

Default:

false

Note:

not shown in the user interface

Note:

disabled

removeShortTracts

Remove short tracts from tractogram

Type:

boolean

Default:

false

shortTractsThreshold

Minimal length for tracts to be conserved.

Type:

number

Default:

100

removeLongTracts

Remove long tracts from tractogram

Type:

boolean

Default:

false

longTractsThreshold

Maximal length for tracts to be conserved.

Type:

number

Default:

100

singleTract

If checked, the module performs single region tractography instead of whole brain

Type:

boolean

Default:

false

referenceTractFile

Path of the reference tract file (.vtk)

Type:

filepath-remote

Default:

not set

Used when:

singleTract is True

displacementFieldFile

Path of the displacement file for transform

Type:

filepath-remote

Default:

not set

Used when:

singleTract is True

dilationRadius

Dilation radius

Type:

number

Default:

2

Used when:

singleTract is True