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jhuguetn / cat12-docker

Docker image of CAT12 (standalone version)
GNU General Public License v3.0
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Error in Example (segmentation of T1w image) #1

Closed lcscosta closed 2 years ago

lcscosta commented 2 years ago

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?

jhuguetn commented 2 years ago

You are completely right @lcscosta, that's a typo in the example command.

I have fixed the README.md file accordingly and I've also updated CAT 12.8 standalone version to the latest stable revision since there were some known -yet unresolved- problems with it (see #2 for details).

I've just tagged and published the latest (r1933) version of the dockerized CAT12 app in Docker Hub. You should be good to go now if you update it as follows,

docker pull jhuguetn/cat12:r1933

Thanks!

lcscosta commented 2 years ago

Thank you, now the docker image is running perfectly.