Summary of what happened:
I’m running fMRIPrep on HCP-Aging 2.0 data using FreeSurfer derivatives from the original HCP pipeline (a modification of FreeSurfer v.6.0) and fMRIPrep is attempting to recreate surfaces (anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3) while recognizing the FreeSurfer directory. fMRIPrep subsequently fails because ${fs_sub}/surf/autodet.gw.stats.lh.dat is not available.
What is triggering fMRIPrep to try and recreate surfaces?
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run \
--cleanenv -B /projects \
/projects/p30952/environment/singularity_images/${FMRIPREP_VER}.simg \
${BIDS_DIR} \
${FMRIPREP_DIR} \
participant --participant-label ${subject} \
-w ${WORK_DIR} \
--omp-nthreads 8 \
--nthreads 12 \
--mem_mb 24000 \
--fs-license-file ${FS_LICENSE} \
--fs-subjects-dir ${BIDS_DIR}/derivatives/freesurfer \
--output-spaces anat fsnative MNI152NLin2009cAsym fsLR fsaverage \
--cifti-output 91k \
--fd-spike-threshold 0.4 \
--dvars-spike-threshold 1.5 \
--dummy-scans 4
Version:
22.1.1
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes
Relevant log outputs (up to 20 lines):
Node Name: fmriprep_22_1_wf.single_subject_HCA6018857_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3
File: /projects/b1145/bram/hcp-aging/derivatives/fmriprep-22.1.1/sub-HCA6018857/log/20230301-094808_98f30593-f88c-4e22-83f6-3c20cbf83641/crash-20230301-102937-brd2241-autorecon3-bfe8f795-56d8-4ad2-a63e-4a34d27191cc.txt
Working Directory: /projects/b1145/bram/work/fmriprep_22_1_wf/single_subject_HCA6018857_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3
Inputs:
FLAIR_file:
T1_files:
T2_file:
args:
big_ventricles:
brainstem:
directive: autorecon3
environ: {}
expert:
flags:
hemi:
hippocampal_subfields_T1:
hippocampal_subfields_T2:
hires:
mprage:
mri_aparc2aseg:
mri_ca_label:
mri_ca_normalize:
mri_ca_register:
mri_edit_wm_with_aseg:
mri_em_register:
mri_fill:
mri_mask:
mri_normalize:
mri_pretess:
mri_remove_neck:
mri_segment:
mri_segstats:
mri_tessellate:
mri_watershed:
mris_anatomical_stats:
mris_ca_label:
mris_fix_topology:
mris_inflate:
mris_make_surfaces:
mris_register:
mris_smooth:
mris_sphere:
mris_surf2vol:
mrisp_paint:
openmp: 8
parallel:
steps:
subject_id: recon_all
subjects_dir:
talairach:
use_FLAIR:
use_T2:
xopts:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.9/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 autorecon3.
Cmdline:
recon-all -autorecon3 -openmp 8 -subjid sub-HCA6018857 -sd /projects/b1145/bram/hcp-aging/derivatives/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels
Stdout:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /projects/b1145/bram/hcp-aging/derivatives/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw-r-- 1 brd2241 p30952 774858 Feb 28 07:21 /projects/b1145/bram/hcp-aging/derivatives/freesurfer/sub-HCA6018857/scripts/recon-all.log
Linux qnode8140 3.10.0-1160.71.1.el7.x86_64 #1 SMP Wed Jun 15 08:55:08 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/projects/b1145/bram/hcp-aging/derivatives/freesurfer/sub-HCA6018857/mri/transforms /projects/b1145/bram/hcp-aging/derivatives/freesurfer/sub-HCA6018857
/projects/b1145/bram/hcp-aging/derivatives/freesurfer/sub-HCA6018857
#--------------------------------------------
#@# WhiteSurfs lh Wed Mar 1 10:29:35 CST 2023
cd /projects/b1145/bram/hcp-aging_nda-pkgs/HCPAgingT1wT2wrsfMRIAllAgePkg/fmriresults01/HCA6018857_V1_MR/T1w/HCA6018857_V1_MR/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 8 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot
ERROR: reading ../surf/autodet.gw.stats.lh.dat
Linux qnode8140 3.10.0-1160.71.1.el7.x86_64 #1 SMP Wed Jun 15 08:55:08 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-HCA6018857 exited with ERRORS at Wed Mar 1 10:29:35 CST 2023
For more details, see the log file /projects/b1145/bram/hcp-aging/derivatives/freesurfer/sub-HCA6018857/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Stderr:
Traceback:
RuntimeError: subprocess exited with code 1.
Thank you!
Bram