Hi everybody,
I am trying to run fmriprep using docker, but I am a new user concerning python and all this environment.
I get an error message concerning recon-all, and it seams that no copy of my nii files could be performed. If someone could give me some advice, that could be great.
Here is both the command line that I entered and the following error message :
fmriprep-docker /home/rjanet/Desktop/SERODOM_BIDS /home/rjanet/Desktop/SERODOM_BIDS_Preprocess/Test_19_mars_v3 participant --participant_label 01 --fs-license-file /home/rjanet/Desktop/Freesurfer_licence --use-syn-sdc --anat-only --n_cpus 1 --output-space fsnative
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.03.1-ce -v /home/rjanet/Desktop/Freesurfer_licence:/opt/freesurfer/license.txt:ro -v /home/rjanet/Desktop/SERODOM_BIDS:/data:ro -v /home/rjanet/Desktop/SERODOM_BIDS_Preprocess/Test_19_mars_v3:/out poldracklab/fmriprep:1.3.1.post2 /data /out participant --participant_label 01 --use-syn-sdc --anat-only --n_cpus 1 --output-space fsnative
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
5 Files, 186.91MB SDL1 T1w
1 - Subject bold
1 - Session
If you have any questions please post on https://neurostars.org/tags/bids
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
190320-09:46:41,791 nipype.workflow WARNING:
SyN SDC correction requires T1 to MNI registration, but "template" is not specified in "--output-space" arguments. Option --use-syn will be cowardly dismissed.
190320-09:46:41,807 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.3.1.post2:
* BIDS dataset path: /data.
* Participant list: ['01'].
* Run identifier: 20190320-094641_54d4d1b2-0521-46ef-a6ed-c05dc0425adc.
/usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Mapping, Set, Iterable
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
190320-09:46:46,121 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the following boilerplate:
Results included in this manuscript come from preprocessing
performed using *fMRIPrep* 1.3.1.post2
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.1.9
(@nipype1; @nipype2; RRID:SCR_002502).
Anatomical data preprocessing
: The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped using `antsBrainExtraction.sh`
(ANTs 2.2.0), using OASIS30ANTs as target template.
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Spatial normalization to the
*ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796]
was performed through nonlinear registration with `antsRegistration`
(ANTs 2.2.0), using brain-extracted versions of both T1w volume
and template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
@fsl_fast].
Many internal operations of *fMRIPrep* use
*Nilearn* 0.5.0 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
### References
Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
Captured warning (<class 'ImportWarning'>): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
Captured warning (<class 'DeprecationWarning'>): Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
Captured warning (<class 'ResourceWarning'>): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
190320-09:46:54,628 nipype.workflow WARNING:
Some nodes demand for more threads than available (1).
Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
Captured warning (<class 'PendingDeprecationWarning'>): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Container
190320-09:46:56,986 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/tmp/work/fmriprep_wf/single_subject_01_wf/bidssrc".
190320-09:46:56,989 nipype.workflow INFO:
[Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
190320-09:46:56,990 nipype.interface WARNING:
No "t2w" images found for sub-<undefined>
190320-09:46:56,990 nipype.interface WARNING:
No "flair" images found for sub-<undefined>
190320-09:46:56,990 nipype.interface WARNING:
No "fmap" images found for sub-<undefined>
190320-09:46:56,990 nipype.interface WARNING:
No "sbref" images found for sub-<undefined>
190320-09:46:56,990 nipype.interface WARNING:
No "roi" images found for sub-<undefined>
190320-09:46:56,996 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc".
190320-09:46:58,746 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions".
190320-09:46:58,748 nipype.workflow INFO:
[Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
190320-09:46:58,829 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions".
190320-09:47:00,958 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1_name".
190320-09:47:00,960 nipype.workflow INFO:
[Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function")
190320-09:47:00,964 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name".
190320-09:47:02,716 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform".
190320-09:47:02,720 nipype.workflow INFO:
[Node] Setting-up "_t1_conform0" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0".
190320-09:47:02,722 nipype.workflow INFO:
[Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform")
190320-09:47:02,748 nipype.workflow INFO:
[Node] Finished "_t1_conform0".
190320-09:47:02,750 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform".
190320-09:47:04,747 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fov_check".
190320-09:47:04,749 nipype.workflow INFO:
[Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function")
190320-09:47:05,193 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fov_check".
/usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'>
imp.find_module('pytest')
190320-09:47:07,40 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config".
190320-09:47:07,42 nipype.workflow INFO:
[Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
190320-09:47:07,66 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config".
190320-09:47:08,757 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip".
190320-09:47:08,760 nipype.workflow INFO:
[Node] Running "t1_skull_strip" ("nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command:
antsBrainExtraction.sh -a /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz -m /tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz -e /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz -d 3 -f /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1
190320-10:15:28,301 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip".
190320-10:15:38,990 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.bids_info" in "/tmp/work/fmriprep_wf/single_subject_01_wf/bids_info".
190320-10:15:38,992 nipype.workflow INFO:
[Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo")
190320-10:15:39,15 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.bids_info".
190320-10:15:51,323 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
190320-10:15:51,327 nipype.workflow INFO:
[Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -i /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz -noskullstrip -openmp 8 -subjid sub-01 -sd /out/freesurfer
190320-10:15:52,843 nipype.workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" (/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1)
190320-10:15:53,251 nipype.workflow ERROR:
Node autorecon1 failed to run on host ddeddedab931.
190320-10:15:53,377 nipype.workflow ERROR:
Saving crash info to /out/fmriprep/sub-01/log/20190320-094641_54d4d1b2-0521-46ef-a6ed-c05dc0425adc/crash-20190320-101553-root-autorecon1-7c06e6db-8ad9-475a-b060-cdd7760dfef7.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon1 -i /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz -noskullstrip -openmp 8 -subjid sub-01 -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
Linux ddeddedab931 3.16.0-0.bpo.4-amd64 #1 SMP Debian 3.16.39-1+deb8u1~bpo70+1 (2017-02-24) x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-01/scripts/recon-all.local-copy'
/out/freesurfer/sub-01
mri_convert /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz /out/freesurfer/sub-01/mri/orig/001.mgz
mri_convert.bin /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz /out/freesurfer/sub-01/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz...
--------------------------------------------------------------------------
GNU libc version: 2.23
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
http://surfer.nmr.mgh.harvard.edu/registration.html
--------------------------------------------------------------------------
Linux ddeddedab931 3.16.0-0.bpo.4-amd64 #1 SMP Debian 3.16.39-1+deb8u1~bpo70+1 (2017-02-24) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-01 exited with ERRORS at Wed Mar 20 10:15:52 UTC 2019
For more details, see the log file /out/freesurfer/sub-01/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 01 (1). Check the HTML reports for details.
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
load_entry_point('fmriprep==1.3.1.post2', 'console_scripts', 'fmriprep')()
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 436, in main
fmriprep_wf.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 599, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 161, in run
self._clean_queue(jobid, graph, result=result))
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 224, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon1 -i /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz -noskullstrip -openmp 8 -subjid sub-01 -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
Linux ddeddedab931 3.16.0-0.bpo.4-amd64 #1 SMP Debian 3.16.39-1+deb8u1~bpo70+1 (2017-02-24) x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-01/scripts/recon-all.local-copy'
/out/freesurfer/sub-01
mri_convert /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz /out/freesurfer/sub-01/mri/orig/001.mgz
mri_convert.bin /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz /out/freesurfer/sub-01/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz...
--------------------------------------------------------------------------
GNU libc version: 2.23
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
http://surfer.nmr.mgh.harvard.edu/registration.html
--------------------------------------------------------------------------
Linux ddeddedab931 3.16.0-0.bpo.4-amd64 #1 SMP Debian 3.16.39-1+deb8u1~bpo70+1 (2017-02-24) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-01 exited with ERRORS at Wed Mar 20 10:15:52 UTC 2019
For more details, see the log file /out/freesurfer/sub-01/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
Sentry is attempting to send 2 pending error messages
Waiting up to 2.0 seconds