Region and Tract Functions

use –action=ana to initiate region or tract functions in [Step T3 Fiber Tracking]

The ana action can use any post-tracking functions listed under “–action=trk”, including delete_repeat,output, export, end_point, ref, connectivity, connectivity_type, connectivity_value, and ROI related commands, such as roi, roi2, …etc. Please check out --action=trk for details.

Examples of Tract Functions:

Convert trk file to txt file

dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz--output=Tracts1.txt

Read track trk file, filter it by ROIs, and output as another trk file

dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts.tt.gz --roi=roi.nii.gz --roi2=roi2.nii.gz --output=filtered_track.tt.gz

Convert trk file to ROI file

dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz --output=ROI.nii.gz

Generate tract density imaging from a trk file.

dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz --export=tdi

Get track statistics from a track file

dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --export=stat    

Get track DKI and ODI statistics from a track file

dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --other_slices=DKI.nii.gz,ODI.nii.gz --export=stat    

Calculate the connectivity using the tractography and ROI files

dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --connectivity=FreeSurferDKT,my_roi.nii.gz,another_roi.nii.gz --connectivity_value=qa,count,ncount --connectivity_type=pass,end

Examples of Region Functions:

Get the statistics of multiple native-space ROIs

dsi_studio --action=ana --source=my.fib.gz --regions=native_space_roi.nii.gz

Get the statistics of multiple MNI-space ROIs

dsi_studio --action=ana --source=my.fib.gz --regions=mni_space_roi.nii.gz

Get statistics from Freesurfer segmented ROIs using subjects T1W to guide the registration

dsi_studio --action=ana --source=my.fib.gz --regions=aparc+aseg.nii.gz --t1t2=subject_t1w.nii.gz

Get statistics from ROIs of the atlas included in the DSI Studio package

dsi_studio --action=ana --source=*.fib.gz --regions=HCP842_tractography:Cingulum_L,HCP842_tractography:Cingulum_R,HCP842_tractography:Corpus_Callosum

Get the statistics from multiple ROIs of an atlas

dsi_studio --action=ana --source=my.fib.gz --atlas=FreeSurferDKT

Core Functions

Parameters	Description
source	specify the fib.gz file

Tract Functions

Parameters	Description
tract	Specify the tract file
output	Use”–output=Tract.txt” to convert the trk file to another format or ROI (assigned output file as NIFTI file)
export	Export additional information related to the fiber tracts

Export tract density images

• Use --export=tdi to generate a track density image in the diffusion space. To output in x2, x3, x4 resolution, use tdi2, tdi3, tdi4 (also applied to the following commands).
• Use --export=tdi_color to generate a track color density image.
• Use --export=tdi_end to output only the endpoint.

Export tract profile

• Use --export=stat to export tract statistics like along tract mean fa, adc, or morphology index such as volume, length, … etc.
• Use --export=report:dti_fa:0:1 to export the tract reports on “fa” values with a profile style at x-direction “0” and a bandwidth of “1”

The profile style can be the following:

• 0: x-direction
• 1: y-direction
• 2: z-direction
• 3: along tracts
• 4: mean of each tract

You can export multiple outputs separated by “,”. For example,

--export=stat,tdi,tdi2 exports track statistics, tract density images (TDI), subvoxel TDI, along tract qa values, and along tract gfa values.

Region Functions

**Do not specify --tract if you want to use the region analysis function **

Parameters	Description
region or regions	specify the NIFTI file of a single ROI (–region) or multiple ROIs (–regions) to export region statistics. If the regions are in the MNI space, add “mni” to the file name (e.g. mni_regions.nii.gz)
t1t2	if the region is derived from a T1W, then specify the t1w image using –t1t2=t1w.nii.gz for registration with the DWI.
atlas	Specify the built-in atlas name for export region statistics

Multiple files can be specified using “+” as the separator. The format can be a txt file or nifti file or from the atlas regions (e.g. –region=FreeSurferDKT:right_precentral+FreeSurferDKT:left_precentral)

The loaded regions can be modified using “smoothing”, “erosion”, “dilation”, “defragment”, “negate”, “flipx”, “flipy”, “flipz”, “shiftx” (shift the roi by 1 in x direction), “shiftnx” (shift the roi by -1 in x direction), “shifty”, “shiftny”, “shiftz”, “shiftnz”.

For example, –region=region.nii.gz,dilate,smoothing –regions=multiple_regions.nii.gz,flipx