Region and Tract Functions

The --action=ana command is used for analyzing fiber tracts, calculating region-based statistics, or performing connectivity analysis within the [Step T3 Fiber Tracking] workflow.

Examples of Tract Functions

The ana action supports post-tracking operations including merging, filtering, and quantifying tracts. Key parameters include connectivity, connectivity_type, other_slices, and export.

Connectivity Analysis

Calculate tract-to-region connectivity using built-in atlases or custom ROI files. Note: connectivity_type defaults to pass (tracts passing through the region). Use end to only count tracts ending within the region.

# Connectivity using built-in atlases
dsi_studio --action=ana --source=my.fz --tract=tract.tt.gz --connectivity=HCP-MMP,Brodmann

# Combining atlases with a custom NIFTI ROI
dsi_studio --action=ana --source=my.fz --tract=bundle.tt.gz --connectivity=HCP-MMP+subcortical.nii.gz

# Using end-point connectivity logic
dsi_studio --action=ana --source=my.fz --tract=*.tt.gz --connectivity=HCP-MMP --connectivity_type=end

Merging and Filtering Tracks

Merge multiple tract files into one:

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

Filter tracts by regions and save the result:

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

Conversion and Statistics

Convert a tract file to a density map or ROI mask:

# Save as NIFTI ROI (binary mask or probability map)
dsi_studio --action=ana --source=avg.mean.fz --tract=Tracts1.tt.gz --output=ROI.nii.gz

# Generate tract density imaging (TDI)
dsi_studio --action=ana --source=avg.mean.fz --tract=Tracts1.tt.gz --export=tdi

Get tract statistics with additional metrics: Use --other_slices to load external maps (like DKI or ODI) for sampling along the tracts.

# Standard statistics (FA, MD, etc.)
dsi_studio --action=ana --source=my.fz --tract=tract.tt.gz --export=stat

# Statistics including external DKI/ODI metrics
dsi_studio --action=ana --source=my.fz --tract=tract.tt.gz --other_slices=DKI.nii.gz,ODI.nii.gz --export=stat

Examples of Region Functions

Region analysis calculates quantitative metrics within specific volumes of interest. If the ROI file contains .mni. in the filename, DSI Studio automatically performs the necessary transformation from MNI space to the subject’s native diffusion space.

Get statistics for native or MNI space ROIs:

dsi_studio --action=ana --source=my.fz --regions=native_roi.nii.gz,mni_space.mni.nii.gz

Get statistics for built-in atlas regions:

dsi_studio --action=ana --source=my.fz --regions=HCP842_tractography:Cingulum_L,HCP842_tractography:Cingulum_R

Examples of Export Functions

To export volume-wide metrics or convert source files, use --action=exp.

Export diffusion metrics from FIB files:

dsi_studio --action=exp --source=subject.fz --export=qa,iso,dti_fa,rd,ad

Convert an SRC file to a 4D NIFTI file:

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

Parameter Definitions

Tract Parameters (--action=ana)

Parameter Description
tract Specifies input tract files (*.trk.gz, *.tt.gz).
output Specifies the output filename. Use .tt.gz for tracts or .nii.gz for ROI/density maps.
export Exports specific tract data (e.g., stat, tdi, tdi_color, tdi_end).
connectivity Lists atlases or NIFTI files for connectivity matrix calculation.
connectivity_type Defines connectivity logic: pass (default) or end.
other_slices Loads external NIFTI maps to be sampled for tract/region statistics.
ref Specifies a reference image to define the grid space for TDI or output ROIs.

Region Parameters (--action=ana)

Parameter Description
regions Specifies NIFTI files or atlas-labeled regions for statistical analysis.
atlas Specifies a built-in atlas to be used for region analysis.

Technical Notes