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:
- Connectivity: The
ana
action supports tract-to-region mapping using theconnectivity
parameter. - Atlas Loading: Atlases are loaded via
atl_load_atlas
and support region extraction usingload_region
. - Tract Statistics: The
get_tract_statistics
function calculates metrics like FA and ADC along tracts. - Region Statistics: The
get_regions_statistics
function aggregates quantitative data for regions.