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 supports various post-tracking functions, including delete_repeat, output, export, end_point, ref, connectivity, and connectivity_type. Additionally, it allows tract-to-region connectivity calculations using built-in atlases or ROI files.

(Available in versions after 2024/10): Calculate the tract-to-region connectivity using tracts and a specified atlas or ROI file.

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

Merging and Filtering Tracks

Merge two trk files and save them to a text file:

dsi_studio --action=ana --source=avg.mean.fz --tract=Tracts1.tt.gz,Tract2.tt.gz --output=Tracts1.txt

Filter a track file by ROIs and save as another trk file:

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

Conversion and Statistics

Convert a trk file to an ROI file:

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

Generate tract density imaging from a trk file:

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

Get track statistics from a track file:

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

Get track DKI and ODI statistics from a track file:

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

Save tracks to a different slice space:

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

Examples of Region Functions:

Get statistics of multiple native-space ROIs:

dsi_studio --action=ana --source=my.fz --other_regions=native_space_roi.nii.gz

Get statistics of multiple MNI-space ROIs:

dsi_studio --action=ana --source=my.fz --other_regions=mni_space_roi.nii.gz

Get statistics from Freesurfer segmented ROIs:

dsi_studio --action=ana --source=my.fz --other_regions=aparc+aseg.nii.gz

Get statistics for ROIs of a built-in atlas:

dsi_studio --action=ana --source=*.fz --region=HCP842_tractography:Cingulum_L,HCP842_tractography:Cingulum_R

Examples of Export Functions:

Export diffusion metrics from FIB files:

dsi_studio --action=ana --source=*.fz --export=qa,iso,dti_fa,rd,ad

Convert an SRC file to a 4D nifti file:

dsi_studio --action=ana --source=test.sz --export=4dnii

Export all fiber orientations in the FIB file:

dsi_studio --action=ana --source=test.fz --export=dirs

Tract Functions Parameters

Parameter Description
tract Specifies the tract file (e.g., *.trk.gz, *.tt.gz). Include mni in the file name for MNI space tracts.
output Assign output file for conversion or ROI generation.
export Export tract-related data (e.g., stat, tdi, tdi_color, tdi_end).

Region Functions Parameters

Parameter Description
other_regions Specifies a NIFTI file of single/multiple ROIs for region statistics. Add mni for MNI-space regions.
atlas Specify a built-in atlas name for region analysis.

Notes from the Source Code: