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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Freesurfer error #941

Closed zswgzx closed 6 years ago

zswgzx commented 6 years ago

docker run -it --rm -v $PWD/ds003:/data:ro -v $PWD/ds003-fmriprep:/out -v $FREESURFER_HOME/license.txt:/opt/freesurfer/license.txt poldrackl ab/fmriprep:latest /data /out/out participant --participant-label 01

Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 11, in load_entry_point('fmriprep==1.0.5', 'console_scripts', 'fmriprep')() File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 270, in main fmriprep_wf.run(plugin_settings) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run self._clean_queue(jobid, graph, result=result)) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue raise RuntimeError("".join(result['traceback'])) RuntimeError: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 487, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 510, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 1016, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 953, in raise_exception ).format(runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon1 -noskullstrip -openmp 3 -subjid sub-01 -sd /out/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/out/freesurfer Actual FREESURFER_HOME /opt/freesurfer -rw-rw-r-- 1 root root 17620 Jan 26 17:34 /out/out/freesurfer/sub-01/scripts/recon-all.log Linux 7e45319255aa 4.13.0-1007-gcp #10-Ubuntu SMP Fri Jan 12 13:56:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/out/freesurfer/sub-01/scripts/recon-all.local-copy'

--------------------------------------------

@# MotionCor Fri Jan 26 18:20:26 UTC 2018

ERROR: no run data found in /out/out/freesurfer/sub-01/mri. Make sure to have a volume called 001.mgz in /out/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 7e45319255aa 4.13.0-1007-gcp #10-Ubuntu SMP Fri Jan 12 13:56:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-01 exited with ERRORS at Fri Jan 26 18:20:26 UTC 2018 For more details, see the log file /out/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

effigies commented 6 years ago

This suggests that you had no T1w input to your FreeSurfer workflow. Is this the only failure you saw? Could you share more of your log?

chrisgorgo commented 6 years ago

Is $PWD/ds003-fmriprep empty? Does $PWD/ds003-fmriprep/out exist?

Best, Chris

zswgzx commented 6 years ago

So far it seemed to be the only problem. The folder $PWD/ds003-fmriprep/out exists but there's no file in sub-01/mri/.

Here's from the $PWD/ds003-fmriprep/out/freesurfer/sub-01/scripts/recon-all.log

/out/out/freesurfer/sub-01 /opt/freesurfer/bin/recon-all -autorecon1 -noskullstrip -openmp 3 -subjid sub-01 -sd /out/out/freesurfer subjid sub-01 setenv SUBJECTS_DIR /out/out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 7e45319255aa 4.13.0-1007-gcp #10-Ubuntu SMP Fri Jan 12 13:56:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 60067 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited

          total        used        free      shared  buff/cache   available

Mem: 15393576 599356 4374760 8912 10419460 14399996 Swap: 0 0 0

######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:17-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:18-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:18-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:24-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/26-18:20:24-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:24-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:24-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:24-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:25-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:25-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:25-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:25-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:25-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:26-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:26-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/26-18:20:26-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 7e45319255aa Platform: Linux PlatformVersion: 4.13.0-1007-gcp CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs #######################################

--------------------------------------------

@# MotionCor Fri Jan 26 18:20:26 UTC 2018

ERROR: no run data found in /out/out/freesurfer/sub-01/mri. Make sure to have a volume called 001.mgz in /out/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 7e45319255aa 4.13.0-1007-gcp #10-Ubuntu SMP Fri Jan 12 13:56:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-01 exited with ERRORS at Fri Jan 26 18:20:26 UTC 2018

effigies commented 6 years ago

Sorry, I meant your fmriprep log.

zswgzx commented 6 years ago

Here it is.

180126-17:40:50,818 workflow IMPORTANT:

Running fMRIPREP version 1.0.5:
  * BIDS dataset path: /data.
  * Participant list: ['01'].
  * Run identifier: 20180126-174050_6437331a-9ce6-4a82-91c7-db4926ab456a.

180126-17:40:51,868 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz" (0.02 GB / 160 TRs). Memory resampled/largemem=0.09/0.13 GB. 180126-17:40:52,478 workflow WARNING: No fieldmaps found or they were ignored, building base workflow for dataset /data/sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz. 180126-17:40:52,723 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180126-17:41:03,752 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_preproc_report_wf.pre_tsnr" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_preproc_report_wf/pre_tsnr". 180126-17:41:03,800 workflow INFO: [Node] Running "pre_tsnr" ("niworkflows.nipype.algorithms.confounds.TSNR") 180126-17:41:04,691 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.validate" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/validate". 180126-17:41:04,694 workflow INFO: [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage") 180126-17:41:04,703 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.validate". 180126-17:41:04,896 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_preproc_report_wf.pre_tsnr". 180126-17:41:05,169 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/bidssrc". 180126-17:41:05,173 workflow INFO: [Node] Running "bidssrc" ("fmriprep.interfaces.bids.BIDSDataGrabber") 180126-17:41:05,175 interface WARNING: No 't2w' images found for sub- 180126-17:41:05,175 interface WARNING: No 'fmap' images found for sub- 180126-17:41:05,176 interface WARNING: No 'sbref' images found for sub- 180126-17:41:05,184 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc". 180126-17:41:06,319 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_split" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_split". 180126-17:41:06,326 workflow INFO: [Node] Running "bold_split" ("niworkflows.nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /data/sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz -t 180126-17:41:08,357 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.gen_ref" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/gen_ref". 180126-17:41:08,361 workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 180126-17:41:08,383 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". 180126-17:41:08,387 workflow INFO: [Node] Running "t1_template_dimensions" ("fmriprep.interfaces.images.TemplateDimensions") 180126-17:41:08,591 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". 180126-17:41:08,868 interface INFO: stderr 2018-01-26T17:41:08.867903:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 180126-17:41:08,869 interface INFO: stderr 2018-01-26T17:41:08.867903:++ Authored by: RW Cox 180126-17:41:08,870 interface INFO: stderr 2018-01-26T17:41:08.870358:++ Coarse del was 10, replaced with 3 180126-17:41:10,74 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". 180126-17:41:10,78 workflow INFO: [Node] Running "t1_name" ("niworkflows.nipype.interfaces.utility.wrappers.Function") 180126-17:41:10,95 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". 180126-17:41:11,979 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform". 180126-17:41:11,987 workflow INFO: [Node] Setting-up "_t1_conform0" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 180126-17:41:11,992 workflow INFO: [Node] Running "_t1_conform0" ("fmriprep.interfaces.images.Conform") 180126-17:41:12,641 workflow INFO: [Node] Finished "_t1_conform0". 180126-17:41:12,645 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform". 180126-17:41:12,720 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_split". 180126-17:41:14,991 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config". 180126-17:41:14,995 workflow INFO: [Node] Running "recon_config" ("fmriprep.interfaces.freesurfer.FSDetectInputs") 180126-17:41:15,3 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config". 180126-17:41:15,899 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip". 180126-17:41:15,905 workflow INFO: [Node] Running "t1_skull_strip" ("niworkflows.nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command: antsBrainExtraction.sh -a /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii.gz -m /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001 -q 1 180126-17:41:32,879 interface INFO: stderr 2018-01-26T17:41:32.879058:++ Max displacement in automask = 0.38 (mm) at sub-brick 12 180126-17:41:32,879 interface INFO: stderr 2018-01-26T17:41:32.879494:++ Max delta displ in automask = 0.16 (mm) at sub-brick 8 180126-17:41:33,801 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.gen_ref". 180126-17:41:35,969 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_hmc_wf.mcflirt" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_hmc_wf/mcflirt". 180126-17:41:35,974 workflow INFO: [Node] Running "mcflirt" ("niworkflows.nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /data/sub-01/func/sub-01_task-rhymejudgment_bold.nii.gz -out /root/src/fmriprep/sub-01_task-rhymejudgment_bold_mcf.nii.gz -reffile /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots 180126-17:42:17,106 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_hmc_wf.mcflirt". 180126-17:42:19,392 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_hmc_wf.normalize_motion" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_hmc_wf/normalize_motion". 180126-17:42:19,394 workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 180126-17:42:19,406 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_hmc_wf.normalize_motion". 180126-17:42:20,16 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_confounds_wf.fdisp" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_confounds_wf/fdisp". 180126-17:42:20,76 workflow INFO: [Node] Running "fdisp" ("niworkflows.nipype.algorithms.confounds.FramewiseDisplacement") 180126-17:42:20,90 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_confounds_wf.fdisp". 180126-17:42:22,737 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_mask" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_mask". 180126-17:42:22,741 workflow INFO: [Node] Running "n4_mask" ("fmriprep.interfaces.nilearn.MaskEPI") 180126-17:42:22,911 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_mask". 180126-17:42:23,986 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 180126-17:42:23,992 workflow INFO: [Node] Running "n4_correct" ("niworkflows.nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_mask/ref_image_mask.nii.gz --output ref_image_corrected.nii.gz 180126-17:42:25,490 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 180126-17:42:26,109 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 180126-17:42:26,118 workflow INFO: [Node] Running "skullstrip_first_pass" ("niworkflows.nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /root/src/fmriprep/ref_image_corrected_brain.nii.gz -f 0.20 -m 180126-17:42:28,368 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 180126-17:42:30,25 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 180126-17:42:30,30 workflow INFO: [Node] Running "skullstrip_first_dilate" ("niworkflows.nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /root/src/fmriprep/ref_image_corrected_brain_mask_dil.nii.gz 180126-17:42:30,368 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 180126-17:42:32,4 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 180126-17:42:32,8 workflow INFO: [Node] Running "skullstrip_first_mask" ("niworkflows.nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /root/src/fmriprep/ref_image_corrected_brain_masked.nii.gz 180126-17:42:32,108 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 180126-17:42:34,14 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 180126-17:42:34,20 workflow INFO: [Node] Running "unifize" ("niworkflows.nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz 180126-17:42:35,518 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 180126-17:42:37,315 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 180126-17:42:37,319 workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 180126-17:42:37,368 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 180126-17:42:38,54 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 180126-17:42:38,60 workflow INFO: [Node] Running "skullstrip_second_pass" ("niworkflows.nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 180126-17:42:38,238 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 180126-17:42:41,18 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 180126-17:42:41,24 workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 180126-17:42:41,82 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 180126-17:42:42,148 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 180126-17:42:42,153 workflow INFO: [Node] Running "combine_masks" ("niworkflows.nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /root/src/fmriprep/ref_image_corrected_brain_mask_maths.nii.gz 180126-17:42:42,247 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 180126-17:42:45,482 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_mni_trans_wf.gen_ref" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_mni_trans_wf/gen_ref". 180126-17:42:45,488 workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 180126-17:42:46,101 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_mni_trans_wf.gen_ref". 180126-17:42:48,144 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 180126-17:42:48,151 workflow INFO: [Node] Running "apply_mask" ("niworkflows.nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /root/src/fmriprep/uni_xform_masked.nii.gz 180126-17:42:48,258 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 180126-18:18:12,381 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip". 180126-18:18:15,24 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_hmc_wf.fsl2itk" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_hmc_wf/fsl2itk". 180126-18:18:15,35 workflow INFO: [Node] Running "fsl2itk" ("fmriprep.interfaces.itk.MCFLIRT2ITK") 180126-18:18:31,923 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_hmc_wf.fsl2itk". 180126-18:18:33,12 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_bold_trans_wf.bold_transform" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_bold_trans_wf/bold_transform". 180126-18:18:33,23 workflow INFO: [Node] Running "bold_transform" ("fmriprep.interfaces.itk.MultiApplyTransforms") 180126-18:20:15,141 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_bold_trans_wf.bold_transform". 180126-18:20:16,397 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1". 180126-18:20:16,404 interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -openmp 3 -subjid sub-01 -sd /out/out/freesurfer 180126-18:20:16,405 workflow INFO: [Node] Running "autorecon1" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon1 -noskullstrip -openmp 3 -subjid sub-01 -sd /out/out/freesurfer 180126-18:20:16,408 interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -openmp 3 -subjid sub-01 -sd /out/out/freesurfer 180126-18:20:17,201 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_bold_trans_wf.merge" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_bold_trans_wf/merge". 180126-18:20:17,212 workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 180126-18:20:21,512 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_bold_trans_wf.merge". 180126-18:20:22,260 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_preproc_report_wf.pos_tsnr" in "/root/src/fmriprep/work/fmriprep_wf/single_subjec t_01_wf/func_preproc_task_rhymejudgment_wf/bold_preproc_report_wf/pos_tsnr". 180126-18:20:22,326 workflow INFO: [Node] Running "pos_tsnr" ("niworkflows.nipype.algorithms.confounds.TSNR") 180126-18:20:25,784 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_preproc_report_wf.pos_tsnr". 180126-18:20:27,40 workflow WARNING: [Node] Error on "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" (/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surf ace_recon_wf/autorecon1) 180126-18:20:27,624 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_task_rhymejudgment_wf.bold_preproc_report_wf.bold_rpt" in "/root/src/fmriprep/work/fmriprep_wf/single_subjec t_01_wf/func_preproc_task_rhymejudgment_wf/bold_preproc_report_wf/bold_rpt". 180126-18:20:27,627 workflow INFO: [Node] Running "bold_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT") 180126-18:20:27,629 niworkflows INFO: Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_rhymejudgment_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images 180126-18:20:27,629 niworkflows INFO: Generating visual report

effigies commented 6 years ago

Can you also rerun with a working directory mounted into your Docker container? The easiest way to do this is to use fmriprep-docker with the -w <workdir> flag.

Then in your working directory, look for fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/_report/report.rst. This should contain a full listing of the inputs to the node. And also look for fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1_conform/_report/report.rst, which should have a list of T1w images that should be the inputs to autorecon1.

effigies commented 6 years ago

It will also simplify things if you use --n-cpus 1 --anat-only --output-space fsnative flags, to run everything in serial (which should help the log be a little more readable), and not to run BOLD preprocessing steps or normalizing the anatomical to MNI. (You can run without these flags later. It will just help for debugging.)

zswgzx commented 6 years ago

This works fine so far. Thank you~