Fmriprep error: msm crashing

Software Support
, ,
1

Summary of what happened:

Hi all,

I’m fairly new to running fmriprep and trying to preprocess data with pre-segmented freesurfer output using singularity. Does anyone know what might be the issue here? Any help much appreciated thanks :slight_smile:

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run --cleanenv \
    -B ${BIDS_DIR}:/data \
    -B ${DERIVATIVES_DIR}:/out \
    -B ${MY_WORK_DIR}:/work \
    ${CONTAINERS_DIR}/fmriprep.sif \
    /data /out participant \
    --fs-license-file ${FS_LICENSE} \
    --nthreads ${N_THREADS} \
    --stop-on-first-crash \
	--skull-strip-t1w skip \
	--output-spaces MNI152NLin2009cAsym anat fsnative func

Version:

PUT VERSION HERE

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

It crashed with the following error in the crash log:
strong text

Stderr:
	** DA[0] has coordsys with intent NIFTI_INTENT_SHAPE (should be NIFTI_INTENT_POINTSET)
	** DA[0] has coordsys with intent NIFTI_INTENT_SHAPE (should be NIFTI_INTENT_POINTSET)
	** DA[0] has coordsys with intent NIFTI_INTENT_SHAPE (should be NIFTI_INTENT_POINTSET)
	** DA[0] has coordsys with intent NIFTI_INTENT_SHAPE (should be NIFTI_INTENT_POINTSET)
	** failed to open GIFTI XML file '/opt/conda/envs/fmriprep/lib/python3.11/site-packages/smriprep/data/atlases/L.refsulc.164k_fs_LR.shape.gii'
	Segmentation fault (core dumped)
Traceback:
	RuntimeError: subprocess exited with code 139.

Scrolling back up the crash log:

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
  File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _msmsulc0.

Cmdline:
	msm --conf=/opt/conda/envs/fmriprep/lib/python3.11/site-packages/smriprep/data/msm/MSMSulcStrainFinalconf --indata=/work/fmriprep_24_1_wf/sub_011_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0/sub-XYZ.L.sulc.native.shape.gii --inmesh=/work/fmriprep_24_1_wf/sub_011_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0/lh.sphere_converted_xformed.surf_mod.surf.gii --out=lh. --refdata=/opt/conda/envs/fmriprep/lib/python3.11/site-packages/smriprep/data/atlases/L.refsulc.164k_fs_LR.shape.gii --refmesh=/opt/conda/envs/fmriprep/lib/python3.11/site-packages/smriprep/data/atlases/fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii --verbose

Screenshots / relevant information:

2

Hi @eyork and welcome to neurostars!

In the future please use the software support post template that is prepopulated. You can see I edited your post for you this time, and there is some additional information that is missing (you can edit your post to add it in).

In addition to the missing info in the template, it would be good to know.

  1. Is this error subject specific or for everyone?
  2. Did fmriprep do freesurfer for you? If not what version did you use?
  3. What operating system are you using? Is this a Linux HPC?
  4. What kind of resources are you devoting to the job?

Best,
Steven

3

Thanks @Steven, I can’t seem to edit the original post so extra info below:

Version 24.1.0 (then 24.1.1)

BIDS validator used

https://bids-standard.github.io/bids-validator/

Linux HPC system

I managed to successfully run it using version 24.1.1 after moving the cache to an area with more storage space (as suggested previously Cleaning up .cache) as these were defaulting to a home area (without much space).

Thanks!