I ran introduction_dataset.ipynb to download the ds000114 dataset. Though I received some INFO messages here, the script seemed to have worked fine (or maybe this is where the bug begins?):
[INFO] Cloning dataset to <Dataset path=/data/ds000114>
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114 to /data/ds000114
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114/.git to /data/ds000114
[INFO] Completed clone attempts for <Dataset path=/data/ds000114>
[INFO] Detected a filesystem without fifo support.
[INFO] Disabling ssh connection caching.
[INFO] access to 1 dataset sibling datalad not auto-enabled, enable with:
| datalad siblings -d "/data/ds000114" enable -s datalad
[INFO] Installing <Dataset path=/data/ds000114> underneath /data/ds000114 recursively
[INFO] Cloning dataset to <Dataset path=/data/ds000114/derivatives/fmriprep>
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114/derivatives/fmriprep/.git to /data/ds000114/derivatives/fmriprep
[INFO] Completed clone attempts for <Dataset path=/data/ds000114/derivatives/fmriprep>
[INFO] Detected a filesystem without fifo support.
[INFO] Disabling ssh connection caching.
[INFO] Cloning dataset to <Dataset path=/data/ds000114/derivatives/freesurfer>
[INFO] Attempting to clone from http://datasets.datalad.org/workshops/nih-2017/ds000114/derivatives/freesurfer/.git to /data/ds000114/derivatives/freesurfer
[INFO] Completed clone attempts for <Dataset path=/data/ds000114/derivatives/freesurfer>
[INFO] Detected a filesystem without fifo support.
[INFO] Disabling ssh connection caching.
I then ran example_preprocessing.ipynb to follow up on that script but this script threw some errors:
210120-14:56:17,119 nipype.workflow ERROR:
could not run node: preproc.datasink.a1.b7
210120-14:56:17,119 nipype.workflow INFO:
crashfile: /home/neuro/nipype_tutorial/notebooks/crash-20210120-141903-neuro-datasink.a1.b7-c3fabc45-48b6-4212-b2e6-3881d91ad1a6.pklz
210120-14:56:17,120 nipype.workflow ERROR:
could not run node: preproc.datasink.a1.b4
210120-14:56:17,121 nipype.workflow INFO:
crashfile: /home/neuro/nipype_tutorial/notebooks/crash-20210120-143347-neuro-datasink.a1.b4-3cd68a5e-fee3-4357-a4f5-a1507f6b497b.pklz
210120-14:56:17,121 nipype.workflow ERROR:
could not run node: preproc.datasink.a1.b3
210120-14:56:17,122 nipype.workflow INFO:
crashfile: /home/neuro/nipype_tutorial/notebooks/crash-20210120-143922-neuro-datasink.a1.b3-8e465547-821b-4e5c-8662-7ccb16c66f80.pklz
210120-14:56:17,123 nipype.workflow ERROR:
could not run node: preproc.datasink.a0.b2
210120-14:56:17,124 nipype.workflow INFO:
crashfile: /home/neuro/nipype_tutorial/notebooks/crash-20210120-144612-neuro-datasink.a0.b2-bd01d507-0793-43ac-b442-70cbf89891ba.pklz
210120-14:56:17,125 nipype.workflow INFO:
***********************************
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-11-e7bed0b326ff> in <module>
----> 1 preproc.run('MultiProc', plugin_args={'n_procs': 4})
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py in run(self, plugin, plugin_args, updatehash)
630 if str2bool(self.config["execution"]["create_report"]):
631 self._write_report_info(self.base_dir, self.name, execgraph)
--> 632 runner.run(execgraph, updatehash=updatehash, config=self.config)
633 datestr = datetime.utcnow().strftime("%Y%m%dT%H%M%S")
634 if str2bool(self.config["execution"]["write_provenance"]):
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py in run(self, graph, config, updatehash)
190
191 self._remove_node_dirs()
--> 192 report_nodes_not_run(notrun)
193
194 # close any open resources
/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py in report_nodes_not_run(notrun)
96 logger.info("***********************************")
97 raise RuntimeError(
---> 98 ("Workflow did not execute cleanly. " "Check log for details")
99 )
100
RuntimeError: Workflow did not execute cleanly. Check log for details
When running the cell after that ( !tree /output/datasink/preproc) one can see that for some subjects the fwhm-8 or fwhm-4 files are missing:
I ran
introduction_dataset.ipynbto download theds000114dataset. Though I received some INFO messages here, the script seemed to have worked fine (or maybe this is where the bug begins?):I then ran
example_preprocessing.ipynbto follow up on that script but this script threw some errors:When running the cell after that (
!tree /output/datasink/preproc) one can see that for some subjects thefwhm-8orfwhm-4files are missing:which apparently leads to a follow-up-errors in the next script
example_1stlevel.ipynb(because these files don't exist they can also not be found):