CMP on singularity cannot execute parcBrainStem and parcHippo BUG

[KyleeCJ]

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:
* anatomical_pipeline.parcellation_stage.parcBrainStem
220924-21:09:05,646 nipype.interface INFO:
b'#--------------------------------------------\n#@# Brainstem Substructures processing Sat Sep 24 21:08:35 EDT 2022\n------------------------------------------\nSetting up environment variables\n---\nLD_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\nFile is empty\nThe file\n "/tmp/MCR_745731584/.mcrCache8.4/segmen0/toolbox/local/matlabrc.m"\ncannot be executed.\n\nOpening log file: /cbica/home/chenj/java.log.59817\n\nLinux 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\n\nT1 Brainstem Substructures exited with ERRORS at Sat Sep 24 21:09:05 EDT 2022\n\nFor more details, see the log file /output_dir/freesurfer-7.1.1/sub-ADNI002S1155_ses-M132/scripts/brainstem-substructures-T1.log'
220924-21:09:05,681 nipype.interface INFO:
b'movvol /output_dir/freesurfer-7.1.1/sub-ADNI002S1155_ses-M132/mri/brainstemSsLabels.v12.mgz\ntargvol /output_dir/freesurfer-7.1.1/sub-ADNI002S1155_ses-M132/mri/rawavg.mgz\noutvol /output_dir/nipype-1.8.0/sub-ADNI002S1155/ses-M132/anatomical_pipeline/parcellation_stage/parcBrainStem/brainstem.nii.gz\ninvert 0\ntal 0\ntalres 2\nregheader 1\nnoresample 0\ninterp nearest (0)\nprecision float (3)\nGdiag_no -1\nSynth 0\nSynthSeed 1664747958\nerror: mghRead(/output_dir/freesurfer-7.1.1/sub-ADNI002S1155_ses-M132/mri/brainstemSsLabels.v12.mgz, -1): could not open file\x00'
220924-21:09:05,682 nipype.interface INFO:
Done

---

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!

[sebastientourbier]

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:v3.1.0

Please could you make the test with this one?

Thank a lot in advance.
Best,
Seb