MRIQC error--Error code 139 and 137

Summary of what happened:

Hi all,

I am currently running MRIQC with the newest version and keep running into crash reports. Sometimes it works and sometimes it doesn’t. See example crash report below. I’m assuming this is due to space/RAM availability (correct me if I’m wrong). How do you keep from constantly having to edit your script for space?

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

#!/usr/bin/bash

#SBATCH -A PAS2302             # Account
#SBATCH -t 05:00:00            # Time limit (HH:MM:SS)
#SBATCH --mem=20G              # Memory allocation per node
#SBATCH --output=slurm-%j.out  # Standard output log file
#SBATCH --error=slurm-%j.err   # Standard error log file

# Read command-line arguments
subject=$1
session=$2


##Note: Make sure you have the most updated version of MRIQC installed. This is version MRIQC v24.1.0.dev0+gd5b13cb5.d20240826 downloaded on 12/21/2024
# Then run your MRIQC command
singularity run --cleanenv \
--bind /fs/ess/PCON0341/projects/TERBO/YT/BIDS_temp:/mnt/bids_dir \
--bind /fs/ess/PCON0341/projects/TERBO/YT/MRIQC:/mnt/output_dir \
/fs/ess/PCON0341/projects/TERBO/containers/mriqc_latest.sif \
/mnt/bids_dir \
/mnt/output_dir \
participant \
--participant_label sub-$subject \
--session-id $session \
--n_procs 20 \
--mem_gb 20 \
-v \
--verbose-reports \
--resource-monitor \
--notrack \
--no-sub \

Version:

MRIQC v24.1.0.dev0+gd5b13cb5.d20240826

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

Singularity .sif file

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

BIDS validator used through Python

Relevant log outputs (up to 20 lines):

Node: mriqc_wf.funcMRIQC.synthstrip_wf.synthstrip
Working directory: /fs/ess/PCON0341/projects/TERBO/TERBO_Pipeline/work/mriqc_wf/funcMRIQC/synthstrip_wf/23c0b96e96590090b543292b164a1c6eafb994bc/synthstrip

Node inputs:

args = <undefined>
border_mm = 1
environ = {}
in_file = /fs/ess/PCON0341/projects/TERBO/TERBO_Pipeline/work/mriqc_wf/funcMRIQC/synthstrip_wf/23c0b96e96590090b543292b164a1c6eafb994bc/pre_n4/clipped_corrected.nii.gz
model = /opt/freesurfer/models/synthstrip.1.pt
num_threads = 1
out_file = <undefined>
out_mask = <undefined>
use_gpu = False

Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
    result['result'] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node synthstrip.

Cmdline:
	synthstrip -b 1 -i /fs/ess/PCON0341/projects/TERBO/TERBO_Pipeline/work/mriqc_wf/funcMRIQC/synthstrip_wf/23c0b96e96590090b543292b164a1c6eafb994bc/pre_n4/clipped_corrected.nii.gz --model /opt/freesurfer/models/synthstrip.1.pt -n 1 -o clipped_corrected_desc-brain.nii.gz -m clipped_corrected_desc-brain_mask.nii.gz
Stdout:

Stderr:
	/opt/conda/lib/python3.11/site-packages/mriqc/synthstrip/cli.py:119: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature.
	  checkpoint = torch.load(modelfile, map_location=device)
	Segmentation fault (core dumped)
Traceback:
	RuntimeError: subprocess exited with code 139.

Screenshots / relevant information:

Getting error codes 137 and 139. Both sem to be similar.


Thanks.

–Subbi M.

Hi @MadhavanSubhashini,

Please reorganize your post to fill out the entire software support template, to give us the information we need to help you better.

Best,
Steven

Hi Steven,

Reformatted to software support template as best as I could.

Thanks.

–Subbi M.

Hi @MadhavanSubhashini,

Please try specifying your own working directory (should be outside BIDS directory; making sure to mount it in the container as well). Also, you should make sure to specify cpu count in the sbatch header as well.

I presume you are on some Linux cluster? Do you know what particular operating system it is?

Best,
Steven

Hi,

I’m using Pitzer Desktop and then connecting to Pitzer via SSH.

Thanks.

–Subbi M.

Hi @MadhavanSubhashini,

I do not know what Pitzer is. It might be an institution-specific thing. Do you know what kind of cluster you are SSH-ing into?

Best,
Steven