_midthickness0 node crash during fmriprep (23.1.4)

Software Support
,
1

Summary of what happened:

I’m using fmriprep (23.1.4) on a movie-watching dataset (N=25, n_run = 5). almost all subjects failed at the node midthickness0

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

I’m running fmriprep thru BABS on HPC (slurm); the whole BABS setup was successful.
here is the fmriprep setup in BABS

singularity run --cleanenv \
	-B ${PWD} \
	-B /om2/user/$(whoami)/images/license.txt:/SGLR/FREESURFER_HOME/license.txt \
	containers/.datalad/environments/fmriprep-23-1-4/image \
	inputs/data/BIDS \
	outputs/fmriprep \
	participant \
	-w ${PWD}/.git/tmp/wkdir \
	--stop-on-first-crash \
	--nthreads 16 \
	--omp-nthreads 8 \
	--mem-mb 40000 \
	--fd-spike-threshold 0.9 \
	--dvars-spike-threshold 5 \
	--fs-license-file /SGLR/FREESURFER_HOME/license.txt \
	--skip-bids-validation \
	--output-layout legacy \
	--force-bbr \
	--notrack \
	--cifti-output 91k \
	-v -v \
	--participant-label "${subid}"

Version:

fmriprep 23.1.4

Environment (Docker, Singularity, custom installation):

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

The input data is BIDS formated see here

Relevant log outputs (up to 20 lines):

here is the crash file from fmriprep

Node: _midthickness0
Working directory: /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0

Node inputs:

args = <undefined>
distance = 0.5
dt = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'}
graymid = <undefined>
in_file = /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/outputs/fmriprep/freesurfer/sub-sid000030/surf/lh.white
nsurfaces = <undefined>
out_name = midthickness
pial = <undefined>
smooth_averages = <undefined>
sphere = sphere
spring = <undefined>
subjects_dir = /opt/freesurfer/subjects
thickness = True
thickness_name = <undefined>
write_iterations = <undefined>

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/lib/python3.10/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 _midthickness0.

Cmdline:
	mris_expand -pial /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial -thickness -thickness_name /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.white 0.5 /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.midthickness
Stdout:
	reading pial surface from /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial
	using distance as a % of thickness
	using thickness file /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness
	expanding surface /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.white by 50.0% of thickness and writing it to /om2/scratch/Sun/yibei/budapest/output/job-32194722-sub-sid000030/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.midthickness
	reading thickness...
Stderr:
	*** buffer overflow detected ***: terminated
	Aborted (core dumped)
Traceback:
	RuntimeError: subprocess exited with code 134.

Screenshots / relevant information:

here is the information about this folder
/fmriprep_23_1_wf/single_subject_sid000030_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/

ls -ls
total 5
1 -rw-r--r-- 1 yibei root  954 Aug 23 22:27 command.txt
1 -rw-r--r-- 1 yibei root  264 Aug 23 22:27 _inputs.pklz
0 lrwxrwxrwx 1 yibei root  123 Aug 23 22:27 lh.pial -> /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/outputs/fmriprep/freesurfer/sub-sid000010/surf/lh.pial
0 lrwxrwxrwx 1 yibei root  125 Aug 23 22:27 lh.sphere -> /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/outputs/fmriprep/freesurfer/sub-sid000010/surf/lh.sphere
0 lrwxrwxrwx 1 yibei root  128 Aug 23 22:27 lh.thickness -> /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/outputs/fmriprep/freesurfer/sub-sid000010/surf/lh.thickness
0 lrwxrwxrwx 1 yibei root  124 Aug 23 22:27 lh.white -> /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/outputs/fmriprep/freesurfer/sub-sid000010/surf/lh.white
2 -rw-r--r-- 1 yibei root 1443 Aug 23 22:27 _node.pklz
0 drwxr-sr-x 2 yibei root 4096 Aug 23 22:27 _report
2 -rw-r--r-- 1 yibei root 2008 Aug 23 22:27 result__midthickness0.pklz

full command

mris_expand -pial /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial -thickness -thickness_name /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.white 0.5 /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.midthickness
2

Hi @yibeichen,

If you run this command outside of the BABS context, do you get the same error? That is,

singularity exec -e --containall -B /om2 /PATH/TO/fmriprep.img \
mris_expand -pial \
/om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial \
-thickness -thickness_name /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness \
/om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.white \
0.5 /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.midthickness

Best,
Steven

3

Thank you! but i got the same error

here is the command

singularity exec -e --containall -B /om2 -B /om2/user/yibei/images/license.txt:/opt/freesurfer/.license /om2/user/yibei/budapest_babs/fmriprep-container/.datalad/environments/fmriprep-23-1-4/image \
> mris_expand -pial \
> /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial \
> -thickness -thickness_name /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness \
> /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.white \
> 0.5 /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.midthickness

if I replace the image path with the one outside of babs/datalad, like /om2/user/yibei/images/fmriprep-23.1.4.simg. the same result/error

here is the result

reading pial surface from /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial
using distance as a % of thickness
using thickness file /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness
expanding surface /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.white by 50.0% of thickness and writing it to /om2/scratch/Sun/yibei/budapest/output/job-32194716-sub-sid000010/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000010_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.midthickness
reading thickness...
*** buffer overflow detected ***: terminated
4

Got it, thanks for checking. In this case, it sounds like a FreeSurfer error. You can try asking the mailing list following instructions here FreeSurferSupport - Free Surfer Wiki.

I have also seen, on very rare occasion, some commands failing due to too long file names. I also wonder if the .git folder having a period in it is causing issues. Can you try copying the necessary files into a less nested directory and run the same command on those files?

1 Like
5

hello hello!! moving files out of .git worked!

here is my command

singularity exec -e --containall -B /om2 -B /om2/user/yibei/images/license.txt:/opt/freesurfer/.license /om2/user/yibei/images/fmriprep-23.1.4.simg \
mris_expand -pial \
/om2/scratch/tmp/yibei/bptest/lh.pial \
-thickness -thickness_name /om2/scratch/tmp/yibei/bptest/lh.thickness \
/om2/scratch/tmp/yibei/bptest/lh.white \
0.5 /om2/scratch/tmp/yibei/bptest/lh.midthickness

here is the message I got (I mean it’s working)

reading pial surface from /om2/scratch/tmp/yibei/bptest/lh.pial
using distance as a % of thickness
using thickness file /om2/scratch/tmp/yibei/bptest/lh.thickness
expanding surface /om2/scratch/tmp/yibei/bptest/lh.white by 50.0% of thickness and writing it to /om2/scratch/tmp/yibei/bptest/lh.midthickness
reading thickness...
min=0.000, parallel=0.0085, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0083, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0325, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0324, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0339, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0734, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.2565, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0320, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0314, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0322, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0322, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0076, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
min=0.000, parallel=0.0083, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
-01: dt=0.0000,   0 negative triangles  VmPeak 1434820
min=0.000, parallel=0.0075, normal=0.0000, spring=0.0000, ashburner=0.000, tsmooth=0.000
ending sse = 4987.868073

now I guess it’s a different issue…
Thank you a lot!

6

okay, I found my colleague’s fmriprep log (used The Script), which also has .git in the path. the _midthickness0 was successful.

[Node] Setting-up "_midthickness0" in "/pwd/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
230816-20:55:40,918 nipype.workflow INFO:
	 [Node] Cached "_midthickness0" - collecting precomputed outputs
7

okay, i think the reason is that the path generated by babs is too long for freesurfer…

8

I also get an error in node _midthickness0 (and also _midthickness1) in fmriprep 23.1.4. My data is in git-annex, but i am not using babs. I believe this didn’t happen when i used 23.1.3

Command inside container (which did have access to a freesurfer license)

 /opt/conda/envs/fmriprep/bin/fmriprep --participant-label sub-001A --nthreads 3 --omp-nthreads 3 --output-spaces MNI152NLin6Asym:res-native MNI152NLin6Sym:res-native --random-seed 03021995 inputs/mri-raw/ . participant

_midthickness0 error:

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/lib/python3.10/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 _midthickness0.

Cmdline:
	mris_expand -pial /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white 0.5 /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness
Stdout:
	reading pial surface from /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial
	using distance as a % of thickness
	using thickness file /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness
	expanding surface /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white by 50.0% of thickness and writing it to /misc/geminis2/twinsmx/datasets/mri_study/mri-derivatives/fmriprep_superdataset/work/fmriprep_23_1_wf/single_subject_001A_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness
	reading thickness...
Stderr:
	*** buffer overflow detected ***: terminated
	Aborted (core dumped)
Traceback:
	RuntimeError: subprocess exited with code 134.
9

Hi @DiegoRg,

Might be the same too long of a filename error, try reducing the path to the working directory.

Best,
Steven

10

hi @yarikoptic this is the issue I mentioned earlier today. Maybe it’s related to Datalad or maybe not?
Thanks!

11

update for this one, my colleague ran fmriprep 23.1.4 on the same dataset thru The Script, and it was successful—no error.
I’m trying to find out what’s happening here by using the process of elimination; @effigies do you think whether this _midthickness0 error is fmriprep related or not?
Thank you!

12

It does not seem like an fMRIPrep problem per se, but an interaction between git-annex, nipype, FreeSurfer, and the specific location of the nipype working directory.

13

so in TheScript, the path is /pwd/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000005_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0, where pwd = /om2/scratch/tmp/jsmentch/fmriprepping/ds003017_project/analysis

In BABS the path is /om2/scratch/Sun/yibei/budapest/output/job-32194541-sub-sid000005/ds/.git/tmp/wkdir/fmriprep_23_1_wf/single_subject_sid000005_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0.

If @djarecka we can make /om2/scratch/Sun/yibei/budapest/output/job-32194541-sub-sid000005/ds/ shorter, then problem should be solved.

14

I’m getting this error also using a singularity container with version 23.1.3
Is there a fix? Which path do I need to make shorter and where? I tried removing the “.” from my file names but I’m still getting the same error. I understand this may be a freesurfer error but none of my freesurfer log files are showing an error.

15

Hi @alrodrig11 and welcome to neurostars!

Do you have particularly long paths in your fMRIPrep command that may lead to the buffer overflow? Sharing more information about your fMRIPrep command would help us debug.

Best,
Steven

16

Hi Steven, Please see the command below. Would I just need to process the data elsewhere to shorten the path?:

export fmriprep_path=/lab-share/Psych-Glahn-e2/Public/neuro/containers/fmriprep-23.1.3
export bids_dir=/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/temp/_$1/
export target_dir=/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/temp/_$1/derivatives/fmriprep23_1_3/
export work_dir=/lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/
export subj=${2}
export fs_license_path=/lab-share/Psych-Glahn-e2/Public/neuro/containers/license.txt

export start_time=`date +%s`

echo $subj

echo About to run:
echo $fmriprep_path ${bids_dir} ${target_dir} participant --participant-label $subj

srun singularity run \
    --cleanenv \
    -B ${bids_dir}:${bids_dir} \
    -B ${target_dir}:${target_dir} \
    -B ${work_dir}:${work_dir} \
    -B ${fs_license_path}:${fs_license_path} \
    $fmriprep_path \
        ${bids_dir} \
        ${target_dir} \
        participant \
        --participant-label ${subj} \
        --omp-nthreads 8 \
        --nthreads 12 \
        --mem_mb 30000 \
        -w ${work_dir} \
        --output-spaces fsaverage fsaverage5 \
        --fs-license-file ${fs_license_path} \
        --skip_bids_validation

echo  ~$(( $((`date +%s` - $start_time)) / 60 / 60 ))
17

Hi @alrodrig11,

You can rename the directory inside the container to shorten it, like the following:

srun singularity run \
    --cleanenv \
    --containall \
    -B ${bids_dir}:/bids  \
    -B ${target_dir}:/out \
    -B ${work_dir}:/work \
    -B ${fs_license_path}:/license.txt \
    $fmriprep_path \
        /bids \
        /out \
        participant \
        --participant-label ${subj} \
        --omp-nthreads 8 \
        --nthreads 12 \
        --mem_mb 30000 \
        -w /work \
        --output-spaces fsaverage fsaverage5 \
        --fs-license-file /license.txt