Freesurfer Autorecon Error Message on 2 participants

Howdy from Texas,

We are trying to run Freesurfer using fmriprep (version 1.5.0) on 118 participants in our study and all have been successfully run except two individuals! We have run BIDS validation on both the participants I have left and there are no errors for them. I am wondering if other users have come across the error message we have or similar messages and have any suggestions on troubleshooting.

Thanks for your help!

Here’s some of the details on our errors:

error message:

fMRIPrep command:
/usr/local/miniconda/bin/fmriprep /data /out participant --notrack --ignore slicetiming -v --skip_bids_validation --mem_mb 8000 --anat-only --output-spaces fsaverage5 --anat-only --participant_label 40653 -w /scratch

Log output:
Node: fmriprep_wf.single_subject_40653_wf.anat_preproc_wf.surface_recon_wf.autorecon1
Working directory: /scratch/fmriprep_wf/single_subject_40653_wf/anat_preproc_wf/surface_recon_wf/autorecon1

Node inputs:

FLAIR_file =
T1_files = [’/data/sub-40653/anat/sub-40653_acq-MPRAGE_run-01_T1w.nii.gz’]
T2_file =
args =
big_ventricles =
brainstem =
directive = autorecon1
environ = {}
expert =
flags = [’-noskullstrip’]
hemi =
hippocampal_subfields_T1 =
hippocampal_subfields_T2 =
hires = False
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 = 5
parallel =
subject_id = sub-40653
subjects_dir = /out/freesurfer
talairach =
use_FLAIR =
use_T2 =
xopts =

Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/”, line 69, in run_node
result[‘result’] =
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/”, line 473, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/”, line 564, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/”, line 649, in _run_command
result =
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/”, line 376, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/”, line 761, in _run_interface
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/”, line 698, in raise_exception
RuntimeError: Command:
recon-all -autorecon1 -noskullstrip -openmp 5 -subjid sub-40653 -sd /out/freesurfer
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /out/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rwx------ 1 root root 17306 Feb 5 21:20 /out/freesurfer/sub-40653/scripts/recon-all.log
Linux 8d54a430679e 4.9.184-linuxkit #1 SMP Tue Jul 2 22:58:16 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
‘/opt/freesurfer/bin/recon-all’ -> ‘/out/freesurfer/sub-40653/scripts/recon-all.local-copy’
#@# MotionCor Thu Feb 6 20:13:17 UTC 2020
ERROR: no run data found in /out/freesurfer/sub-40653/mri. Make sure to
have a volume called 001.mgz in /out/freesurfer/sub-40653/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also:
Linux 8d54a430679e 4.9.184-linuxkit #1 SMP Tue Jul 2 22:58:16 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-40653 exited with ERRORS at Thu Feb 6 20:13:17 UTC 2020

For more details, see the log file /out/freesurfer/sub-40653/scripts/recon-all.log
To report a problem, see

Standard error:

Return code: 1

ERROR: no run data found in /out/freesurfer/sub-40653/mri. Make sure to
have a volume called 001.mgz in /out/freesurfer/sub-40653/mri/orig.

It looks like it failed to copy your NIfTI file in. Possibly there was a cancelled run, a filesystem glitch, or you ran out of space/hit a quota?

I would suggest removing /out/freesurfer/sub-40653 and re-running fresh to see if that resolves the issue.

Thank you so much for your help! I went ahead and deleted the previous output and working directory and reran the participant in Freesurfer. The next error I saw said to update the license so I went ahead and updated the license and reran the participant. This ended up giving me the same error that no run data was found so I started over again. Even with these efforts, the latest error after that one was the initial error message listed in this post. My next step is to try to run the participant on an updated fmriprep version. Do you have any other suggestions? Thank you!