Error CAT 12 segmentation

Bugs
1

Hi everyone, I have a problem with CAT 12 segmentation. I have my T1, and on my Windows pc, it works correctly. My university gave me a quite good pc, so that I don't have to destroy mine. In this new pc I have Linux and Matlab2017b. I tried to run CAT 12 segmentation but I have this error:

CAT Preprocessing error for spm_cat12:

Curvature file "/home/duma/.brainstorm/tmp/cat12/surf/lh.defects.spm_cat12" does not exist!
I read that someone else had the same problem. Did anyone find a solution for this bug?
Thanks

2

@gianmarcoduma Please post the full error log.

@CGaser Any suggestion?

3

Hi Francois, this is the full erro log on that appears on the matlab command window. I read that also another brainstorm user, if I'm not wrong Monalisa, had the same problem in november. Hope this could help

CAT Preprocessing error for spm_cat12:

Curvature file "/home/duma/.brainstorm/tmp/cat12/surf/lh.defects.spm_cat12" does not exist!

673 - read_curv
95 - cat_io_FreeSurfer
636 - cat_surf_createCS
663 - cat_main
786 - cat_run_job
15 - cat_run_newcatch
720 - run_job
434 - cat_run
29 - cfg_run_cm
1717 - local_runcj
972 - cfg_util
469 - fill_run_job
247 - spm_jobman
231 - Compute
265 - ComputeInteractive
27 - process_segment_cat12
1031 - @(h,ev)process_segment_cat12('ComputeInteractive',iSubject,iAnatomy)

Print 'Graphics' figure to:
/home/duma/.brainstorm/tmp/cat12/report/catreport_spm_cat12.pdf
24-Mar-2020 10:16:49 - Failed 'CAT12: Segmentation'
Error using cat_io_FreeSurfer>read_curv (line 673)
Curvature file "/home/duma/.brainstorm/tmp/cat12/surf/lh.defects.spm_cat12" does not exist!

In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_io_FreeSurfer.m" (v1286), function "read_curv" at line 673.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_io_FreeSurfer.m" (v1286), function "cat_io_FreeSurfer" at line 95.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_surf_createCS.m" (v1435), function "cat_surf_createCS" at line 636.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_main.m" (v1446), function "cat_main" at line 663.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_run_job.m" (v1435), function "cat_run_job" at line 786.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 15.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_run.m" (v1439), function "run_job" at line 720.
In file "/home/duma/Desktop/MatLab_toolbox/spm12/toolbox/cat12/cat_run.m" (v1439), function "cat_run" at line 434.

The following modules did not run:
Failed: CAT12: Segmentation

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing
the exact #job as displayed in this error message)

Running job #1

4

Reference to the other post you're mentioning:

I'm sorry, I can't help you much with this...
Let's wait for some input from @CGaser

5

Hi Gianmarco,
does this error also occur with other data sets? It looks as if a temporary file could not be read and was probably not saved during preprocessing.
The only other idea I have (if the error is always occurring) is that there are some issue with the folder name with the leading dot in ".brainstorm".
Best,
Christian