Fmriprep-docker_recon-all

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

Thanks for sharing your command and error message!

I’ve had this happen to me before too. I believe the solution is to download a newer/valid freesurfer license file and pass that file into the fmriprep-docker call, fmriprep uses freesurfer 6.0.1 currently.

Is /home/rjanet/Desktop/Freesurfer_licence a file or a directory that contains the desired file? The input to --fs-license-file should be a file (not a directory).

Hope this helps!
James

1 Like

I fixe the --fs-licence-file to be a file and not a directory but I still get an error message:

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'>
190320-14:53:45,532 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
190320-14:53:47,876 nipype.workflow INFO:
	 [Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/tmp/work/fmriprep_wf/single_subject_01_wf/bidssrc".
190320-14:53:47,878 nipype.workflow INFO:
	 [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
190320-14:53:47,879 nipype.interface WARNING:
	 No "t2w" images found for sub-<undefined>
190320-14:53:47,879 nipype.interface WARNING:
	 No "flair" images found for sub-<undefined>
190320-14:53:47,879 nipype.interface WARNING:
	 No "fmap" images found for sub-<undefined>
190320-14:53:47,879 nipype.interface WARNING:
	 No "sbref" images found for sub-<undefined>
190320-14:53:47,880 nipype.interface WARNING:
	 No "roi" images found for sub-<undefined>
190320-14:53:47,886 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc".
190320-14:53:49,623 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".
190320-14:53:49,625 nipype.workflow INFO:
	 [Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
190320-14:53:49,705 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions".
190320-14:53:52,150 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".
190320-14:53:52,153 nipype.workflow INFO:
	 [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function")
190320-14:53:52,157 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name".
190320-14:53:53,649 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".
190320-14:53:53,652 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".
190320-14:53:53,655 nipype.workflow INFO:
	 [Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform")
190320-14:53:53,682 nipype.workflow INFO:
	 [Node] Finished "_t1_conform0".
190320-14:53:53,685 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform".
190320-14:53:55,651 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".
190320-14:53:55,653 nipype.workflow INFO:
	 [Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function")
190320-14:53:56,97 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')
190320-14:53:57,979 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".
190320-14:53:57,981 nipype.workflow INFO:
	 [Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
190320-14:53:58,7 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config".
190320-14:53:59,657 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".
190320-14:53:59,661 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
190320-15:22:02,32 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip".
190320-15:22:11,739 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".
190320-15:22:11,741 nipype.workflow INFO:
	 [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo")
190320-15:22:11,846 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_01_wf.bids_info".
190320-15:22:15,844 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".
190320-15:22:15,856 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon1 -noskullstrip -openmp 8 -subjid sub-01 -sd /out/freesurfer 
190320-15:22:15,856 nipype.workflow INFO:
	 [Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -noskullstrip -openmp 8 -subjid sub-01 -sd /out/freesurfer 
190320-15:22:15,858 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon1 -noskullstrip -openmp 8 -subjid sub-01 -sd /out/freesurfer 
190320-15:22:17,494 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)
190320-15:22:17,744 nipype.workflow ERROR:
	 Node autorecon1 failed to run on host 32ce947597c3.
190320-15:22:17,853 nipype.workflow ERROR:
	 Saving crash info to /out/fmriprep/sub-01/log/20190320-145332_b8e72945-c399-4bf5-a4aa-af3b86252177/crash-20190320-152217-root-autorecon1-fc39f730-2087-4b24-8b9b-ea6116087feb.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 -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
-rw-rw-r-- 1 root root 51471 Mar 20 13:29 /out/freesurfer/sub-01/scripts/recon-all.log
Linux 32ce947597c3 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'
#--------------------------------------------
#@# MotionCor Wed Mar 20 15:22:17 UTC 2019
ERROR: no run data found in /out/freesurfer/sub-01/mri. Make sure to
have a volume called 001.mgz in  /out/freesurfer/sub-01/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux 32ce947597c3 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 15:22:17 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 -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
-rw-rw-r-- 1 root root 51471 Mar 20 13:29 /out/freesurfer/sub-01/scripts/recon-all.log
Linux 32ce947597c3 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'
#--------------------------------------------
#@# MotionCor Wed Mar 20 15:22:17 UTC 2019
ERROR: no run data found in /out/freesurfer/sub-01/mri. Make sure to
have a volume called 001.mgz in  /out/freesurfer/sub-01/mri/orig.
If you have a second run of data call it 002.mgz, etc.
Linux 32ce947597c3 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 15:22:17 UTC 2019


Standard error:

Return code: 1

hmm, did you delete the freesurfer directory here (/home/rjanet/Desktop/SERODOM_BIDS_Preprocess/Test_19_mars_v3) before running the process again?

If you did delete that directory before running docker again and still got that error, perhaps it would be useful to specify a working directory (with -w) where all the intermediate files will be stored in case we need to go diving through the intermediate outputs to diagnose the problem.

1 Like

So I change the directory and add a working directory.

fmriprep-docker /home/rjanet/Desktop/SERODOM_BIDS /home/rjanet/Desktop/SERODOM_BIDS_Preprocess/Test_19_mars_v4 participant --participant_label 01 --fs-license-file /home/rjanet/Desktop/Freesurfer_licence/license.txt --use-syn-sdc --anat-only --n_cpus 1 --output-space fsnative --w /home/rjanet/Desktop/SERODOM_bids_Preprocess/TMP2

Now I have another error:

Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 101, in _python_exit
    thread_wakeup.wakeup()
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 89, in wakeup
    self._writer.send_bytes(b"")
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 183, in send_bytes
    self._check_closed()
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 136, in _check_closed
    raise OSError("handle is closed")
OSError: handle is closed
Sentry is attempting to send 0 pending error messages

Any suggestion?
Thanks a lot !

Hi @RemiJanet

I’ve had this issue before, and got around by requesting for more mem, and I always keep my --n_cpus 8.

Look at your original post, perhaps try increasing your --n_cpus ?

PS. I use the singularity approach to run fMRIPrep.

Cheers,
Thapa

Thanks, I will try to increase --n_cpus to 8 and I’ll let you know how it goes.

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