Question about --mask / --apply_mask with --action=rec in DSI Studio

[Julian Cramer]

Hi Frank,

We're using DSI Studio in an automated DTI pipeline for mouse and have a question about applying masks in CLI mode.

Our reconstruction command looks something like this:

dsi_studio \
  --action=rec \
  --source=<dwi.sz> \
  --mask=<AIDAmri_BET_mask.nii.gz> \
  --apply_mask \
  --method=1 \
  --other_output=all \
  --output=<output.fz> \
  --check_btable=0 \
  --make_isotropic=0

According to the log, the mask is opened correctly:

mask=<AIDAmri_BET_mask.nii.gz>

open <AIDAmri_BET_mask.nii.gz>

Nevertheless, the FA/MD/AD/RD NIfTI files exported later with --action=exp do not appear to be strictly limited to this mask. We continue to find non-zero values outside the BET mask in the exported maps. Most importantly, there seems to be an issue with the BET/masking performed by DSI Studio itself; please see the attached image.

We are currently using:

DSI Studio Hou version, Jul 21 2026.

Thank you very much and best regards,

Julian

[Frank Yeh]

Sorry about the bug. Could you post the log output of CLI? I will check to see if anything goes wrong.

Frank

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[Frank Yeh]

I committed a fix. Please update DSI Studio and see if the new update works for you.

Frank