Hi, I am trying to run fmriprepdocker on my data but it kept crashing or having errors.
To give you a background, my data is a multi-session& multi-run structure (sub/ ses-1,2,3/run-1,2), after validating my data, I used the following command line but either I can only get the report of the first session, or the report of only the first run of the first session. Also some error messages.
fmriprep-docker /this is the path to the input/runcode --longitudinal --participant-label sub-2115 --fs-license-file /fmri_data_fmriprep/license.txt --use-aroma --output-space T1w template --work-dir /this is the path to wok dir/runcode/working --fs-no-reconal
Hi , thanks for the reply. I pasted the log file for the crashes here. Actually there are lots of crashes and I only included 2 here. Waiting for your reply.
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 472, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 563, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 643, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 377, in run
outputs = self.aggregate_outputs(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 455, in aggregate_outputs
predicted_outputs = self._list_outputs()
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/utils.py”, line 558, in _list_outputs
glob(os.path.join(os.getcwd(), outbase + ext)))
FileNotFoundError: [Errno 2] No such file or directory
2)Node: fmriprep_wf.single_subject_2115_wf.func_preproc_ses_2_task_BID_run_02_wf.bold_hmc_wf.fsl2itk
Working directory: /scratch/fmriprep_wf/single_subject_2115_wf/func_preproc_ses_2_task_BID_run_02_wf/bold_hmc_wf/fsl2itk