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, atlas-overlap statistics, 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

Tract overlap with a built-in atlas

Use --overlap=<atlas-name> to voxelize one tract and report its intersections with every nonempty label of a built-in atlas:

dsi_studio --action=ana \
  --source=my.fz \
  --tract=CST.tt.gz \
  --overlap=HCP-MMP

The output is the ordinary region-statistics table for the temporary tract-atlas intersections. Each nonempty atlas label is a result column; atlas labels with zero overlap are omitted. The table is written as:

CST.tt.gz.overlap.txt

The overlap filename is based on the tract filename passed to post-processing. --output does not redirect this overlap table.

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 for operations that support them; atlas-overlap analysis is intended for one tract bundle at a time.
`--overlap`	Exact built-in atlas name used to calculate tract-atlas overlap statistics. Zero-overlap labels are omitted.
`--output`	Output tractography or NIFTI filename, depending on the requested operation. It does not redirect the tract `--overlap` table, which is saved as `<tract-file>.overlap.txt`.
`--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

Region overlap with a built-in atlas

For statistics-only localization, --overlap=<atlas-name> directly intersects one source region with every label of the requested built-in atlas. It does not require loading atlas labels as separate regions:

dsi_studio --action=ana \
  --source=my.fz \
  --region=tumor.nii.gz \
  --overlap=CHA \
  --output=tumor_CHA.txt

--overlap requires exactly one source region. Each nonempty atlas label becomes a result column and zero-overlap labels are omitted. The rows are the same quantitative measurements used by normal region statistics, including voxel count and volume.

Without --output, region statistics are written to:

<source>.statistics.txt

If --output is a directory, DSI Studio writes the default statistics filename into that directory. If it is a filename, that filename is used and .txt is appended when needed.

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.
`--overlap`	Exact built-in atlas name used to calculate region-atlas overlap statistics. Requires exactly one loaded source region.
`--atlas`	Built-in atlas selection for region analysis when required by the workflow.
`--output`	Region-statistics output filename or directory. Defaults to `<source>.statistics.txt`; `.txt` is appended to an explicit filename when needed.

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