CAT12 segmentation error: No executable modules

jary224 · December 4, 2022, 3:19am

Hello,

When running brainstorm and attempting to perform T1 MRI segmentation with CAT12 to obtain cortex surfaces, I receive the following error:

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
** >process_segment_cat12.m>Compute at 359
** >process_segment_cat12.m>ComputeInteractive at 442
** >process_segment_cat12.m at 28
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_segment_cat12,'ComputeInteractive',iSubject,iAnatomy) at 3085

I'm not sure how to resolve this error so any advice is appreciated, thank you. Both Brainstorm and CAT12/SPM are up to date.

Francois · December 5, 2022, 3:08pm

By itself, this error is difficult to interpret.
Please copy-paste the full text output you get between the moment you start the CAT12 computation and the error.

Both Brainstorm and CAT12/SPM are up to date.

Please specify if both CAT12 and SPM12 were installed as Brainstorm plugins, or if you installed them manually on your computer.

@CGaser

jary224 · December 5, 2022, 8:09pm

Hello Francois,

Thank you for the response but I have resolved the issue by unloading SPM. I believe I had two versions separate versions installed on different paths and that is what was causing the difficulties.

ErikaHS · February 1, 2023, 4:10pm

Hi! I had the same error than you. Could you tell me how to solve it? Thank you so much!

jary224 · February 1, 2023, 7:54pm

In this particular case, I was able to solve the issue by unloading the plug ins and reloading them after restarting brainstorm. Hope this helps.

MLisicki · March 13, 2023, 4:09am

Hi!

I've tried this, but it doesn't seem to work.

Here's what I get:

BST> Plugin spm12 already loaded: C:\Program Files\SPM\spm12
BST> Adding plugin cat12 to path: C:\Users\marco\.brainstorm\plugins\cat12\cat12
BST> Executing callback LoadedFcn: LinkCatSpm(2);
BST> Creating symbolic link: mklink /D "C:\Program Files\SPM\spm12\toolbox\cat12" "C:\Users\marco\.brainstorm\plugins\cat12"
BST> SPM12 template found: C:\Program Files\SPM\spm12\tpm\TPM.nii
BST> Checking latest online version for cat12...
BST> Processing dependencies: cat12 requires: spm12 
BST> Plugin cat12 already loaded: C:\Users\marco\.brainstorm\plugins\cat12
BST> Emptying temporary directory...

SPM12: spm_cat12 (vCAT12.8.2)                      01:03:34 - 13/03/2023
========================================================================

   _______  ___  _______    
  |  ____/ / _ \ \_   _/   
  | |___  / /_\ \  | |     Computational Anatomy Toolbox
  |____/ /_/   \_\ |_|     CAT12.8.2 - https://neuro-jena.github.io

 CAT default file:
	C:\Users\marco\.brainstorm\plugins\cat12\cat12\cat_defaults.m

Item tools: No field(s) named
cat
Item tools: No field(s) named
cat
Your version of CAT12 is up-to-date.

***************************************************************************
** Error: Line 472:  spm_jobman>fill_run_job (line 472)
** 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
** >process_segment_cat12.m>Compute at 361
** >process_segment_cat12.m>ComputeInteractive at 444
** >process_segment_cat12.m at 28
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_segment_cat12,'ComputeInteractive',iSubject,iAnatomy) at 3089

Your help would be much appreciated!

Best,
Marco

Francois · March 13, 2023, 8:45am

The problem seems to be CAT not being identified as a SPM toolbox.

Maybe unload and reload SPM and CAT plugins?
If it doesn't work uninstall and reinstall them both.

Check your Matlab path to make sure that you don't have SPM installed anywhere else on your computer.
Execute which cat12 and which spm12 in your Matlab command window: they should both be in the $HOME/.brainstorm/plugins folder.
Try starting spm12, close it. Then start cat12, close it. Can you start both?

MLisicki · March 15, 2023, 3:53am

Thanks for your suggestions, François.
I went through all of them but couldn't work around this issue.
Guess I'll just go the freesurfer way.

Cheers,
Marco

Francois · March 15, 2023, 9:13am

If you can install and start spm12 and cat12 manually, not as Brainstorm plugins but as it is recommended in the respective websites, you could:

Run CAT12 independently from Brainstorm and later import the output in Brainstorm with the menu "Import anatomy folder", just like with FreeSurfer but changing the file format to import.
If it works, tell Brainstorm to use your manually installed versions: https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins#Example:_FieldTrip

MLisicki · March 16, 2023, 4:05am

Dear François,

Thanks to your suggestions it's finally working!
I downloaded CAT straight from its website and saved it into SPM toolboxes folder.
Then I chose custom install and selected the folder in Brainstorm.

Many thanks for your advice!

Tanmay · April 3, 2023, 7:44am

Hi,
There is CAT12 segmentation error i have attached the ss

Francois · April 3, 2023, 8:16am

@Tanmay I moved your message here as it possibly the same error.

Tanmay · April 3, 2023, 9:09am

Hi
i tried unloading and reloading both the plugins but on reloading the cat12 i am getting this error
error2

Francois · April 3, 2023, 9:24am

This is also addressed on this forum:
https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12#Troubleshooting

Tanmay · April 3, 2023, 10:42am

Thanks Francois!
It worked.

Junichi_Uemura · December 20, 2023, 12:45am

Hi Cassani,
Thank you for your repeated responses.
I received another error messages. Please give me advice.

Best,
Jun

** Error: Line 459: error: spm_jobman>fill_run_job (line 459)
** No executable modules, but still unresolved dependencies or incomplete module inputs.
**
** Call stack:
** >spm_jobman.m>fill_run_job at 459
** >spm_jobman.m at 231
** >process_segment_cat12.m>Compute at 359
** >process_segment_cat12.m>ComputeInteractive at 442
** >process_segment_cat12.m at 28
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_segment_cat12,'ComputeInteractive',iSubject,iAnatomy) at 3051
**

Raymundo.Cassani · December 20, 2023, 1:11am

@Junichi_Uemura, I moved your message as it is the same error as in this post.

Verify if SPM and CAT12 are installed as Brainstorm plugins.
Try to unloading and reloading both plugins
Copy-paste the full text output you get between the moment you start the CAT12 computation and the error.

Junichi_Uemura · December 27, 2023, 8:59am

Hi Cassani,
Thank you for your kind reply. It's finally working.
I followed this reply. At first, it didn't work well. But I tried to do unloading and reloading again and again, then it works.

Best,
Jun