jhuguetn / cat12-docker Goto Github PK

Updating CAT to version 12.8 (revision 1904) made containerized application execution fail (issue reported to CAT12 users group). Issue seems unrelated to the containerization and mostly related to CAT itself. Error trace below,

 ___  ____  __  __
/ __)(  _ \(  \/  )
\__ \ )___/ )    (   Statistical Parametric Mapping
(___/(__)  (_/\/\_)  SPM12 - https://www.fil.ion.ucl.ac.uk/spm/ 
 
Undefined function or variable 'mysubs_fields'. 
 
Error in cfg_branch (line 59)
Error in cfg_getfile>reg_filter (line 1185)
Error in cfg_getfile (line 177)
Error in spm_select (line 115)
Error in spm_select (line 110)
Error in spm_select (line 97)
Error in spm_jobman (line 173)
Error in spm_standalone (line 95)
MATLAB:UndefinedFunction

Update

That issue should be now fixed and CAT standalone should work in newer revisions of version 12.8. Try updating to newer stable revision of CAT 12.8 and check if it fixes the problem.

Thanks for this tool.

I pulled it today and am testing it using singularity. Segmentation appears to work ok but when running surface segmentation, I receive the following:

  Create initial surface                                          /bin/bash: /opt/spm/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/CAT.glnx86/CAT_SeparatePolygon: Permission denied

WARNING: Surface processing will not work because
(1) CAT binaries are not compatible to your system or
(2) File permissions are not correct (for unix use chmod a+x) or
(3) Antivirus software in Windwos or Gatekeeper in MAC OS is blocking to execute binaries

Hi @jhuguetn, thank you for creating a docker image for CAT12.

Unfortunately I got an error with the example in documentation.

I run the command sudo docker run -it --rm -v /home/user/data:/data jhuguetn/cat12 -b /opt/spm/standalone/cat_standalone_segment.txt /data/t1.nii

and got the following output

`
grep: /opt/spm/standalone/cat_standalone_segment.txt: No such file or directory
grep: /opt/spm/standalone/cat_standalone_segment.txt: No such file or directory
grep: /opt/spm/standalone/cat_standalone_segment.txt: No such file or directory
grep: /opt/spm/standalone/cat_standalone_segment.txt: No such file or directory
Setting up environment variables
LD_LIBRARY_PATH is .:/opt/mcr/v93/runtime/glnxa64:/opt/mcr/v93/bin/glnxa64:/opt/mcr/v93/sys/os/glnxa64:/opt/mcr/v93/sys/opengl/lib/glnxa64
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/connectivity/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/external/signal/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/external/stats/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/fileio/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/forward/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/inverse/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/plotting/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/preproc/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/specest/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/statfun/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/trialfun/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/fieldtrip/utilities/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/ricoh_meg_reader/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/external/yokogawa_meg_reader/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/matlabbatch/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/toolbox/DAiSS/private
Warning: Private directories not allowed in MATLAB path: /opt/spm/spm12_mcr/home/gaser/spm12/toolbox/TSSS/private
SPM12, version 7771 (standalone)
MATLAB, version 9.3.0.713579 (R2017b)

/ )( _ ( / )
_ \ )/ ) ( Statistical Parametric Mapping
(/(_) (_//_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/
Undefined function or variable 'mysubs_fields'.
Error in cfg_branch (line 59)
Error in cfg_getfile>reg_filter (line 1185)
Error in cfg_getfile (line 177)
Error in spm_select (line 115)
Error in spm_select (line 110)
Error in spm_select (line 97)
Error in spm_jobman (line 173)
Error in spm_standalone (line 95)
MATLAB:UndefinedFunction
`
Changing /opt/spm/standalone/cat_standalone_segment.txt to /opt/spm/standalone/cat_standalone_segment.m avoid the error of No such file or directory.

Do you have any idea how to solve this undefined function problem?