Region and Tract Analysis

Use --action=ana to analyze existing tractography or regions with a FIB file. It supports tract statistics, tract density imaging, ROI filtering, connectivity analysis, and region-based quantitative measurements.

Tract Analysis Examples

Tract statistics

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

Load additional scalar maps, such as DKI or NODDI outputs, and include them in tract statistics:

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

Merge tract files

dsi_studio --action=ana \
  --source=avg.mean.fz \
  --tract=tract1.tt.gz,tract2.tt.gz \
  --output=merged_tracts.tt.gz

Filter a tract by ROI

dsi_studio --action=ana \
  --source=avg.mean.fz \
  --tract=tracts.tt.gz \
  --roi=roi.nii.gz \
  --output=filtered_tract.tt.gz

Export tract density imaging

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

Convert tractography to a NIFTI region/density map

dsi_studio --action=ana \
  --source=avg.mean.fz \
  --tract=tract.tt.gz \
  --output=tract_region.nii.gz

Connectivity Analysis

Calculate connectivity using built-in atlases or NIFTI parcellations:

dsi_studio --action=ana \
  --source=my.fz \
  --tract=tract.tt.gz \
  --connectivity=HCP-MMP,Brodmann

Use endpoint-based connectivity instead of the default pass-through definition:

dsi_studio --action=ana \
  --source=my.fz \
  --tract=tract.tt.gz \
  --connectivity=HCP-MMP \
  --connectivity_type=end

Parameter	Description
--tract	Input tractography files (.tt.gz or .trk.gz). Multiple files can be comma-separated.
--output	Output tractography or NIFTI filename, depending on the requested operation.
--export	Tract output such as stat, tdi, tdi_color, or tdi_end.
--connectivity	Comma-separated built-in atlas names or NIFTI parcellations used for connectivity calculation.
--connectivity_type	pass (default) or end.
--other_slices	Additional NIFTI maps sampled for tract/region statistics.
--ref	Reference image defining the output grid for TDI or NIFTI output.

Region Analysis

Analyze one or more native-space regions:

dsi_studio --action=ana \
  --source=my.fz \
  --region=roi1.nii.gz,roi2.nii.gz

Analyze regions from a labeled NIFTI file or built-in atlas:

dsi_studio --action=ana --source=my.fz --region=labels.nii.gz:Hippocampus

dsi_studio --action=ana --source=my.fz --region=AAL2:Hippocampus_L

Common --region forms include:

--region=mask.nii.gz
--region=labels.nii.gz
--region=labels.nii.gz:Hippocampus
--region=AAL2:Hippocampus_L
--region=roi1.nii.gz,roi2.nii.gz

Parameter	Description
--region	NIFTI region files or atlas-qualified region names used for quantitative statistics.
--atlas	Built-in atlas selection for region analysis when required by the workflow.

If a NIFTI region filename contains mni, DSI Studio treats it as an MNI-space image and maps it to native diffusion space when the required transformation is available. A labeled NIFTI can use a matching .txt or .json label file; FreeSurfer aparc/aseg files use the built-in FreeSurfer lookup table.

When a native-space region has a different image geometry from the FIB file, use --other_slices to load its anatomical reference so DSI Studio can apply the corresponding registration.

Exporting Whole-Volume Metrics

Whole-volume diffusion metrics are exported with --action=exp, for example:

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