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.

Merge two trk files and save it to a txt file

dsi_studio --action=ana --source=avg.mean.fib.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 --roi=roi.nii.gz --roi2=roi2.nii.gz

Convert trk file to ROI file

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

Generate tract density imaging from a trk file.

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

Get track statistics from a track file

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

Get track statistics from a mni-space track file

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

Get track DKI and ODI statistics from a track file

dsi_studio --action=ana --source=my.fib.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 --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 (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.
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

Export tract profile

The profile style can be the following:

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)