CAT12 does not preproces all images and fails to create symbolic links

I have a dataset that contains 270 T1-weighted images that I want to preprocess using CAT12. However, CAT12 only manages to preprocess 180 out of 270 images. Though, in the console it says:

  Processed successfully:     180 volume(s)
  Processed with error:         0 volume(s)

In case of warnings and errors please check the correct position
of the AC by using the SPM display function.

I checked the err directory which is created by CAT12 and I can only find information (.txt, .xml, .pdf) for 12 files. I also checked the .log files. It seems that CAT12 is unable to copy files and/or create symbolic links for some files:

CAT Preprocessing error for sub-A00036503_ses-20060101_acq-mprage_run-01_T1w:
Bad tissue contrast (BG=49.76, CSF=109.18, GM=108.51, WM=139.88): 
  This can be the result of (i) an improper SPM segmentation caused by 
  failed affine registration, (ii) improper image properties with low 
  contrast-to-noise ratio, or (iii) by preprocessing error. 
  Please check image orientation and quality. 
  372 - cat_main_gintnorm1639
  113 - cat_main1639
  884 - cat_run_job1639
   33 - cat_run_newcatch
  865 - run_job
  455 - cat_run

Print 'Graphics' figure to: 
{ Error using cat_check_system_output (line 27)
ln: failed to create symbolic link
Operation not supported

Error in cat_run_newcatch (line 239)

Error in cat_run>run_job (line 865)

Error in cat_run (line 455)
varargout{1} = run_job(job);

Can someone help with this? Pinging @Christian_Gaser here, maybe he knows what’s going on?

Dear @JohannesWiesner,

you have split the calculation of your data into 3 jobs and in one job there occur errors and this will stop preprocessing of the remaining files. There is an option in CAT12 to move on if errors occur. However, I suspect that you are using an older CAT12 version (please always provide your release number). The “bad tissue contrast” error should occur more rarely with the newest release.



Hi @Christian_Gaser, I am using CAT12.7 (r1720) from 2020-09-21. If I am not mistaken, the ‘continue with next subject’-option is set as default in this version? The only changes from my side where selecting the images and splitting the task into 18 jobs.

Hi @JohannesWiesner,

then I could only suggest to check file permissions and use a clean installation of the newest version and try again processing of the remaining files.



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The solution to the problem was quite straight forward. As reported in the error message, MATLAB was not able to create symbolic links (ln: failed to create symbolic link), because my IT department simply hadn’t allowed it on the filesystem I am working on. After enabling this, everything worked.