Region and Tract Functions

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

Examples of Tract Functions:

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.

(Versions after 2024/10) Calculate the tract-to-region connectivity using the tracts and built-in atlas or ROI file

dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --connectivity=HCP-MMP,Brodmann
dsi_studio --action=ana --source=my.fib.gz --tract=bundle1.tt.gz,bundle2.tt.gz,bundle3.tt.gz --connectivity=HCP-MMP+subcortical.nii.gz
dsi_studio --action=ana --source=my.fib.gz --tract=*.tt.gz --connectivity=HCP-MMP

Merge two trk files and save it to a txt file

dsi_studio --action=ana --source=avg.mean.fib.gz --tract=Tracts1.tt.gz,Tract2.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 statistics from a mni-space track file

dsi_studio --action=ana --source=my.fib.gz --tract=tract_mni.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    

*Save tracks to a difference slice space

dsi_studio --action=ana --source=my.fib.gz --tract=tract.tt.gz --ref=t1w.nii.gz --output=tract_in_t1w.tt.gz

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 (including ‘mni’ in the file name tells DSI Studio that this is an MNI space region)

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

Examples of Export Functions:

Get the diffusion metrics from fib files

dsi_studio --action=ana --source=*.gqi.1.25.fib.gz --export=qa,iso,dti_fa,rd,ad

Export all fiber orientations in the fib file

dsi_studio --action=ana --source=test.fib.gz --export=dirs

Convert an SRC file to a 4D nifti file

dsi_studio --action=ana --source=test.src.gz --export=4dnii

Core Functions

Parameters	Description
source	specify the fib.gz file

Tract Functions

Parameters	Description
tract	Specify the tract file	Specify tractography file (.trk.gz .tt.gz). If the tracts are in the MNI-space, include `mni` in the file name (e.g. tract_mni.tt.gz)
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

Export Functions

If no tract or region is specified, then DSI Studio will export data from the FIB file or SRC file.

use “–export=qa,iso,dti_fa,ad,rd,md” to export the diffusion metrics as nifti files.

use “–export=dirs” to export all fiber orientations as an 4D nifti file. The fiber orientations are unit vectors stored in the 4th dimension. Since each voxel may have multiple fiber orientations, each voxel can have, for example, 15 values, which is 5 fibers x 3 vector dimensions. The storage sequence is [x direction of 1st fiber][y direction of 1st fiber][z direction of 1st fiber][x direction of 2nd fiber][y direction of 2nd fiber]. You can also export the major fiber orientation only by –export=dir0 or the secondary by –export=dir1.

use “–export=4dnii” to export DWI data and b table from an SRC file. The output is a 4d nifti file and text files recording the b-table.

use the following matlab codes to get the values for x, y, and z directions:

I = load_nii('sample.dirs.nii.gz');
dir_x = squeeze(I.img(:,:,:,1));
dir_y = squeeze(I.img(:,:,:,2));
dir_z = squeeze(I.img(:,:,:,3)); 

use “–export=dir0” to export only the 1st (primary) fiber orientation as an 4D nifti file. The fiber orientations are stored in the 4th dimension. The sequence is [x of 1st fiber][y of 1st fiber]. To export the 2nd fiber, use “–export=dir1”.

You can combine multiple export targets. (e.g., –export=dirs,dir0,dir1,fa0,fa1)