Fmriprep: recon-all Not running

Software Support
1

Hi all,

I’m trying to apply fmriprep on my own dataset. But the recon-all step fail to be performed, with following outputs:

230925-03:28:40,251 nipype.workflow INFO:
         fMRIPrep workflow graph with 3936 nodes built successfully.
230925-03:28:49,564 nipype.workflow IMPORTANT:
         fMRIPrep started!
230925-03:29:08,744 nipype.workflow WARNING:
         Some nodes exceed the total amount of memory available (112.97GB).
230925-03:29:38,470 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_1_wf.single_subject_3001_wf.anat_preproc_wf.fs_isrunning" in "/scratch/fmriprep_23_1_wf/single_subject_3001_wf/anat_preproc_wf/fs_isrunning".
230925-03:29:38,640 nipype.workflow INFO:
         [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function>
230925-03:29:38,651 nipype.workflow INFO:
         [Node] Finished "fs_isrunning", elapsed time 0.007126s.
230925-03:37:13,110 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_1_wf.single_subject_3001_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/scratch/fmriprep_23_1_wf/single_subject_3001_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
230925-03:37:13,285 nipype.workflow INFO:
         [Node] Executing "autorecon1" <smriprep.interfaces.freesurfer.ReconAll>
230925-03:37:13,320 nipype.interface INFO:
         recon-all complete : Not running
230925-03:37:13,347 nipype.interface INFO:
         recon-all complete : Not running
230925-03:37:13,549 nipype.workflow INFO:
         [Node] Finished "autorecon1", elapsed time 0.260315s.
230925-03:38:37,267 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_1_wf.single_subject_3001_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/scratch/fmriprep_23_1_wf/single_subject_3001_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
230925-03:38:37,434 nipype.workflow INFO:
         [Node] Executing "skull_strip_extern" <niworkflows.interfaces.freesurfer.FSInjectBrainExtracted>
230925-03:38:37,769 nipype.workflow INFO:
         [Node] Finished "skull_strip_extern", elapsed time 0.332891s.
230925-03:41:08,298 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_1_wf.single_subject_3001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.gcareg" in "/scratch/fmriprep_23_1_wf/single_subject_3001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/gcareg".
230925-03:41:08,476 nipype.workflow INFO:
         [Node] Executing "gcareg" <smriprep.interfaces.freesurfer.ReconAll>
230925-03:41:08,486 nipype.interface INFO:
         recon-all complete : Not running
230925-03:41:08,492 nipype.interface INFO:
         recon-all complete : Not running
230925-03:41:08,702 nipype.workflow INFO:
         [Node] Finished "gcareg", elapsed time 0.222166s.
230925-03:41:10,305 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_23_1_wf.single_subject_3001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/scratch/fmriprep_23_1_wf/single_subject_3001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
230925-03:41:10,479 nipype.workflow INFO:
         [Node] Executing "autorecon2_vol" <smriprep.interfaces.freesurfer.ReconAll>
230925-03:41:10,523 nipype.interface INFO:
         recon-all complete : Not running
230925-03:41:10,565 nipype.interface INFO:
         recon-all complete : Not running
230925-03:41:10,772 nipype.workflow INFO:
         [Node] Finished "autorecon2_vol", elapsed time 0.289923s.

recon-all-rh.txt (111.2 KB)

I’ve also uploaded the log file for further details. I cannot figure out the bugs here. Hope someone can help me.

BTW, here’s the command line I used:
ffmriprep-docker E:\BIDS\ E:\fmriprep-out\ --omp-nthreads 16 --fs-license-file D:\coderepo\freesurfer\license.txt -w E:\fmriprep-intermediate\ --ignore slicetiming

Thanks!

2

Hi @Shimmering,

That message usually indicates that recon-all was already run. Are there precomputed freesurefer outputs already there?

Best,
Steven

4

Shoot, I’ve deleted the previous results…

But is it normal that “recon-all -s sub-3001 exited with ERRORS” was shown in the recon-all-rh.txt file (as attached)?
recon-all-rh.txt (111.2 KB)

5

Ah sorry didn’t see the log file. Maybe related to other reported problems with mris_curvature: Problems running autorecon2_vol: ERROR: Executable 'mris_curvature -all-info failed! Is it missing from the distribution?' - #2 by aileen

In the meantime you can try running recon-all outside of fMRIPrep and then feeding those outputs to fMRIPrep.

6

Actually I found there were two places giving error messages in my log file.

The first chunk:
230925-01:32:40,115 nipype.workflow INFO:
[Node] Finished “_autorecon_surfs0”, elapsed time 2257.157103s.
230925-01:32:40,127 nipype.workflow WARNING:
[Node] Error on “_autorecon_surfs0” (/bighome/yxiong5/fmriprep_workdir/fmriprep_23_1_wf/single_subject_003_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0)
230925-01:32:40,645 nipype.workflow ERROR:
Node _autorecon_surfs0 failed to run on host compute-16-3.local.
230925-01:32:40,653 nipype.workflow ERROR:
Saving crash info to /bids_output/sub-003/log/20230924-204719_9489f0e4-1178-4ed7-8921-66deccc44009/crash-20230925-013240-yxiong5-_autorecon_surfs0-d1e98b1a-8010-4755-bc62-a1fe48cdfa04.txt
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 _autorecon_surfs0.

The second chunk:
230925-01:40:58,712 nipype.workflow INFO:
[Node] Finished “_autorecon_surfs1”, elapsed time 0.975268s.
230925-01:40:58,721 nipype.workflow WARNING:
[Node] Error on “_autorecon_surfs1” (/bighome/yxiong5/fmriprep_workdir/fmriprep_23_1_wf/single_subject_003_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1)
230925-01:40:59,122 nipype.workflow ERROR:
Node _autorecon_surfs1 failed to run on host compute-16-3.local.
230925-01:40:59,125 nipype.workflow ERROR:
Saving crash info to /bids_output/sub-003/log/20230924-204719_9489f0e4-1178-4ed7-8921-66deccc44009/crash-20230925-014059-yxiong5-_autorecon_surfs1-34b5378f-1f1c-4a5c-94b6-c5c2a9a7db74.txt
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 _autorecon_surfs1.

Cmdline:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 4 -subjid sub-003 -sd /bids_output/sourcedata/freesurfer
Stdout:
fs-check-version --s sub-003 --o /tmp/tmp.PbtdCk
Mon Sep 25 01:40:58 CDT 2023

setenv SUBJECTS_DIR /bids_output/sourcedata/freesurfer
cd /bighome/yxiong5/fmriprep_workdir/fmriprep_23_1_wf/single_subject_003_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1
/opt/freesurfer/bin/fs-check-version --s sub-003 --o /tmp/tmp.PbtdCk
-rwxrwxr-x 1 root root 18565 Aug  4  2022 /opt/freesurfer/bin/fs-check-version

freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
$Id$
Linux compute-16-3.local 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
pid 10740
Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
bstampfile exists /bids_output/sourcedata/freesurfer/sub-003/scripts/build-stamp.txt
Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /bids_output/sourcedata/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux compute-16-3.local 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
ERROR: Executable 'mris_curvature -all-info failed! Is it missing from the distribution?'

Stderr:
Killed
Traceback:
RuntimeError: subprocess exited with code 1.