I’m not sure what to make of an error I’m encountering while re-running the latest version of fmriprep (1.0.0-rc10). This is also my first time converting the dicoms with heudiconv (previously, I had just been calling dcm2niix directly), so that is another confound (the dataset did at least pass the online bids validator).
Call:
module load singularity/singularity-2.4
singularity run poldracklab_fmriprep_latest-2017-11-10-3e683742db3e.img /data/vtf/ /data/vtf/derivatives/ participant -w /data/vtf/derivatives/work/ --fs-license-file /license.txt --output-space template T1w fsaverage fsnative --nthreads 14 --mem_mb 143360 --participant-label 01 02
(note: singularity image created with singularityware/docker2singularity)
output (the derivatives/fmriprep/logs folder is empty, and the derivatives/fmriprep/sub-01 folder hadn’t been created):
Running fMRIPREP version 1.0.0-rc10:
- Participant list: [‘01’, ‘02’].
- Run identifier: 20171115-191753_190b20ab-5d74-49a1-af7f-e84deeb76876.
171115-19:18:40,665 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-01_bold.nii.gz.
171115-19:18:50,894 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-02_bold.nii.gz.
171115-19:19:01,160 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-03_bold.nii.gz.
171115-19:19:11,423 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-04_bold.nii.gz.
171115-19:19:21,667 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-05_bold.nii.gz.
171115-19:19:31,769 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-06_bold.nii.gz.
171115-19:19:42,29 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-07_bold.nii.gz.
171115-19:19:52,341 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-con_run-08_bold.nii.gz.
171115-19:20:02,202 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-loc_run-01_bold.nii.gz.
171115-19:20:09,539 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-loc_run-02_bold.nii.gz.
171115-19:20:19,487 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-ret_run-01_bold.nii.gz.
171115-19:20:29,653 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-01/func/sub-01_task-ret_run-02_bold.nii.gz.
171115-19:20:45,5 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-01_bold.nii.gz.
171115-19:20:51,784 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-02_bold.nii.gz.
171115-19:21:01,9 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-03_bold.nii.gz.
171115-19:21:09,802 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-04_bold.nii.gz.
171115-19:21:19,411 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-05_bold.nii.gz.
171115-19:21:27,558 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-06_bold.nii.gz.
171115-19:21:33,881 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-07_bold.nii.gz.
171115-19:21:43,527 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-con_run-08_bold.nii.gz.
171115-19:21:52,763 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-loc_run-01_bold.nii.gz.
171115-19:22:02,10 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-loc_run-02_bold.nii.gz.
171115-19:22:11,251 workflow WARNING:
No fieldmaps found or they were ignored, building base workflow for dataset /home/ps52a/data/vtf/sub-02/func/sub-02_task-ret_run-01_bold.nii.gz.
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
load_entry_point(‘fmriprep==1.0.0rc10’, ‘console_scripts’, ‘fmriprep’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 228, in main
create_workflow(opts)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 347, in create_workflow
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py”, line 591, 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 182, in run
self._send_procs_to_workers(updatehash=updatehash, graph=graph)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py”, line 260, in _send_procs_to_workers
if self._local_hash_check(jobid, graph):
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 333, in _local_hash_check
hash_exists, _, _, _ = self.procs[jobid].hash_exists()
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 278, in hash_exists
hashed_inputs, hashvalue = self._get_hashval()
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 445, in _get_hashval
hash_method=self.config[‘execution’][‘hash_method’])
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 572, in get_hashval
hash_files=hash_files)))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 587, in _get_sorteddict
hash_files=hash_files)))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 587, in _get_sorteddict
hash_files=hash_files)))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 587, in _get_sorteddict
hash_files=hash_files)))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 594, in _get_sorteddict
hash_files=hash_files))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py”, line 600, in _get_sorteddict
os.path.isfile(objekt)):
File “/usr/local/miniconda/lib/python3.6/genericpath.py”, line 30, in isfile
st = os.stat(path)
ValueError: embedded null byte