Fmriprep FileNotFoundError

1

Hi all,

I’m having the following error for a few subjects in a dataset that I have already processed before.

FileNotFoundError: /working/tinnitus_scratch30/fmriprep/work/fmriprep_wf/single_subject_MINN188_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1/result__parcstats1.pklz

Does anyone have any idea of what could be causing it? I’m running fMRIPrep-20.1.0rc3

Thank you.

Here is the crash file output:

Node: fmriprep_wf.single_subject_MINN188_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats
Working directory: /working/tinnitus_scratch30/fmriprep/work/fmriprep_wf/single_subject_MINN188_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats

Node inputs:

FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon-hemi
environ = {}
expert = <undefined>
flags = ['-nohyporelabel']
hemi = ['lh', 'rh']
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = <undefined>
mprage = <undefined>
mri_aparc2aseg = <undefined>
mri_ca_label = <undefined>
mri_ca_normalize = <undefined>
mri_ca_register = <undefined>
mri_edit_wm_with_aseg = <undefined>
mri_em_register = <undefined>
mri_fill = <undefined>
mri_mask = <undefined>
mri_normalize = <undefined>
mri_pretess = <undefined>
mri_remove_neck = <undefined>
mri_segment = <undefined>
mri_segstats = <undefined>
mri_tessellate = <undefined>
mri_watershed = <undefined>
mris_anatomical_stats = <undefined>
mris_ca_label = <undefined>
mris_fix_topology = <undefined>
mris_inflate = <undefined>
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 3
parallel = <undefined>
steps = <undefined>
subject_id = recon_all
subjects_dir = <undefined>
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 94, in nodelist_runner
    result = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 493, in run
    emptydirs(outdir, noexist_ok=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 802, in emptydirs
    os.makedirs(path)
  File "/usr/local/miniconda/lib/python3.7/os.py", line 221, in makedirs
    mkdir(name, mode)
FileExistsError: [Errno 17] File exists: '/working/tinnitus_scratch30/fmriprep/work/fmriprep_wf/single_subject_MINN188_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1386, in _run_interface
    self.config["execution"]["stop_on_first_crash"]
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1250, in _collate_results
    for i, nresult, err in nodes:
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 99, in nodelist_runner
    result = node.result
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 217, in result
    op.join(self.output_dir(), "result_%s.pklz" % self.name)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 291, in load_resultfile
    raise FileNotFoundError(results_file)
FileNotFoundError: /working/tinnitus_scratch30/fmriprep/work/fmriprep_wf/single_subject_MINN188_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1/result__parcstats1.pklz
2

Please try upgrading to 21.0.1 with a new work directory and try again.

3

Hi Steven,
Thank you for your prompt reply. The reason why I haven’t upgrated fmriprep is because I’m running in a big dataset which I’ve run 80% of the subjects already. Would upgrading be the best option even though some subjects were processed with a different version?

4

If you haven’t already began to analyze data, which seems to be the case for you, I would personally upgrade. Make sure you do not reuse any derivatives or working directories from older runs (besides FreeSurfer, if it is version 6).

5

For this issue, it appears to be a filesystem synchronization issue, a race condition (is it possible you were running this same subject on multiple nodes?), or possibly the disk has run out of space. I would try re-running before scrapping and starting over.

If that fails, then I would try re-running this subject with 20.1.4, which should be able to reuse the working directory from 20.1.0rc3.

If that fails, then I would try using 21.0.1 on this subject with a new working directory. And if that succeeds, I would strongly consider re-running all of your subjects.

6

Thanks @Steven and @effigies for the help! I will try that.