SPM12 Skull Stripping - Tissue Probability Map error?

Bugs
,
1

Hi,

I’m a relatively new user, downloaded Brainstorm only a few weeks ago, the standalone version, installed using Matlab Runtime R2023a. After encountering the issue below, I’ve updated my version of Brainstorm to the latest, and the issue persists.

I am unable to run SPM12 skull stripping. I receive the following output:

BST> SPM12 template found: /Users/tara/.brainstorm/defaults/spm/TPM.nii
BST> SPM12 template found: /Users/tara/.brainstorm/defaults/spm/TPM.nii
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).
Item 'Tissue probability map', field 'val': Number of matching files (0) less than required (1).

***************************************************************************
** Error: Line 472:  spm_jobman>fill_run_job
** No executable modules, but still unresolved dependencies or incomplete module inputs.
** 
** Call stack:
** >spm_jobman.m>fill_run_job at 472
** >spm_jobman.m at 247
** >mri_normalize_segment.m at 100
** >mri_skullstrip.m at 168
** >bst_call.m at 26
** >tree_callbacks.m>MriSkullStrip at 3930
** >tree_callbacks.m>@(h,ev)MriSkullStrip(MriFile,sSubject.Anatomy(sSubject.iAnatomy).FileName,'SPM') at 3244
** 
***************************************************************************


***************************************************************************
** Error: Could not perform skull stripping.
** 
***************************************************************************

I receive this same output when I try to run this process on default anatomy data as well as tutorial data.

I’ve inspected the TPM.nii file and as far as I can tell there is nothing wrong with it. It is a 4D volume as described here: Chapter 4: Segmentation — Andy's Brain Book 1.0 documentation

Thank you!

2

@chinmay.chinara Can you please check this?

3

Hi @tpalnitkar,

I ran the latest standalone version (05-Jan-2026) on Windows and was not able to reproduce this issue.

Could you please provide more information about your setup? This can be obtained with the menu Help > System info in the main Brainstorm window.

4

Thank you @chinmay.chinara for looking into this.

=== Brainstorm === 
  Version :        3.260105
  Release :        260105
  Variant :        standalone
  Plugins :        brain2mesh* ct2mrireg* iso2mesh* neuromaps* gedai* brainentropy* blackrock* neuroelectrics*
  :                xdf* fastica* libsvm* mvgc* picard* derivelfp* nirstorm* mcxlab-cl*
  :                gardel* mia*
 
=== Brainstorm directories === 
*** Directory paths may contain sensitive information, check before sharing *** 
  Brainstorm :     /Users/tara/Library/Application Support/.mcrCache9.14/bst_ja0/bst_javabuil
  DataBase   :     /Users/tara/brainstorm/brainstorm_db
  Bst_User   :     /Users/tara/.brainstorm
  Temporary  :     /Users/tara/.brainstorm/tmp
 
=== Matlab === 
  Matlab version : R2023a (9.14)
  Java version   : 1.8
 
=== System === 
  OS name   :      macOS 12.7.1 (x86_64)
  OS type   :      mac64
  Mem total :      16384 MiB
  Mem avail :      10486 MiB

Is the Brainstorm location a problem? Not sure why it’s looking in /Library/Application Support - I unzipped (and open brainstorm3.command) from a sub-folder of my home directory (distinct from brainstorm_db).

5

@tpalnitkar thank you for sharing. I was able to reproduce the error at my end. The Brainstorm location is not an issue. I will check and get back to you.

6

@tpalnitkar there is a similar thread for this issue:

https://neuroimage.usc.edu/forums/t/cat12-segmentation-error-no-executable-modules

EDIT: Even from the screenshot you shared, it seems the spm12 plugin is missing.

7

@tpalnitkar, this is now fixed, and the fix is included in the latest binary (24-Apr-2026)

Please download the latest binary from: https://neuroimage.usc.edu/bst/download.php

8

Thank you so much @Raymundo.Cassani, with the new binary everything worked for me. And thank you @chinmay.chinara for looking into this!

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