sebastientourbier
commented
1 year ago Dear @KyleeCJ ,
Thank you for reporting this.
Last week, I managed to release a new version of CMP3. Could you try it and let me know if this works?
Note that a singularity image of CMP3 is also built along with the docker image and can be accessed as follows:
$ singularity pull library://connectomicslab/default/connectomemapper-bidsapp:v3.1.0Please could you make the test with this one?
Thank a lot in advance. Best, Seb
Dear sebastien,
Greetings.
I am using the singularity image to run CMP3 on cluster, and found error saying this for both parcBrainStem and parcHippo stage:
220924-21:08:37,453 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 2720.68/2720.88, Free processors: 0/1. Currently running:
I further checked the log file in the freesurfer and it says:
OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux 2117fmn001 3.10.0-1062.el7.x86_64 #1 SMP Wed Aug 7 18:08:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
setenv SUBJECTS_DIR /output_dir/freesurfer-7.1.1 cd /output_dir/nipype-1.8.0/sub-ADNI002S1155/ses-M132/anatomical_pipeline/parcellation_stage/parcBrainStem /opt/freesurfer/bin/segmentBS.sh sub-ADNI002S1155_ses-M132 /output_dir/freesurfer-7.1.1
@# Brainstem Substructures processing Sat Sep 24 21:08:35 EDT 2022
Setting up environment variables
LD_LIBRARY_PATH is .:/opt/freesurfer/MCRv84//runtime/glnxa64:/opt/freesurfer/MCRv84//bin/glnxa64:/opt/freesurfer/MCRv84//sys/os/glnxa64:/opt/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib/fsl/5.0:/lib/x86_64-linux-gnu:/usr/lib:/usr/local/lib:/.singularity.d/libs File is empty The file "/tmp/MCR_745731584/.mcrCache8.4/segmen0/toolbox/local/matlabrc.m" cannot be executed.
Opening log file: /cbica/home/chenj/java.log.59817
Linux 2117fmn001 3.10.0-1062.el7.x86_64 #1 SMP Wed Aug 7 18:08:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
T1 Brainstem Substructures exited with ERRORS at Sat Sep 24 21:09:05 EDT 2022
Could you please check why this would cause the error? The image is converted from a local docker image and it does not have that error when I tried to run it locally. In addition, if I change the tag in the configuration file to false to skip these two steps it will also be successful to finish the entire pipeline. Thank you very much!