Thank you so much !
I will keep digging on it using --help but just wanted show you the error message(below) by using the extended command you suggested…
Thanks
BL
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Running fMRIPREP version 1.0.15:
* BIDS dataset path: /data.
* Participant list: [‘201’].
* Run identifier: 20180620-005232_a663fb02-b343-4c3d-bae4-1efcbb0171d1.
180620-00:52:33,978 workflow IMPORTANT:
Creating bold processing workflow for “/data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmAP_run-01_bold.nii.gz” (0.40 GB / 1072 TRs). Memory resampled/largemem=1.62/5.95 GB.
180620-00:52:34,828 workflow IMPORTANT:
Slice-timing correction will be included.
180620-00:52:35,43 workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmAP_run-01_bold.nii.gz found.
180620-00:52:35,838 workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
180620-00:52:37,699 workflow IMPORTANT:
Creating bold processing workflow for “/data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmAP_run-04_bold.nii.gz” (0.38 GB / 1009 TRs). Memory resampled/largemem=1.54/5.41 GB.
180620-00:52:38,483 workflow IMPORTANT:
Slice-timing correction will be included.
180620-00:52:38,705 workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmAP_run-04_bold.nii.gz found.
180620-00:52:39,552 workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
180620-00:52:41,428 workflow IMPORTANT:
Creating bold processing workflow for “/data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmPA_run-02_bold.nii.gz” (0.40 GB / 1072 TRs). Memory resampled/largemem=1.61/5.92 GB.
180620-00:52:42,89 workflow IMPORTANT:
Slice-timing correction will be included.
180620-00:52:42,316 workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmPA_run-02_bold.nii.gz found.
180620-00:52:43,84 workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
180620-00:52:44,989 workflow IMPORTANT:
Creating bold processing workflow for “/data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmPA_run-03_bold.nii.gz” (0.40 GB / 1063 TRs). Memory resampled/largemem=1.60/5.84 GB.
180620-00:52:45,718 workflow IMPORTANT:
Slice-timing correction will be included.
180620-00:52:45,934 workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /data/sub-201/ses-01/func/sub-201_ses-01_task-DofG_acq-MB43mmPA_run-03_bold.nii.gz found.
180620-00:52:46,676 workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
load_entry_point(‘fmriprep==1.0.15’, ‘console_scripts’, ‘fmriprep’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 314, in main
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py”, line 594, in run
self._write_report_info(self.base_dir, self.name, execgraph)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py”, line 619, in _write_report_info
op.join(report_dir, ‘index.html’))
File “/usr/local/miniconda/lib/python3.6/shutil.py”, line 121, in copyfile
with open(dst, ‘wb’) as fdst:
PermissionError: [Errno 13] Permission denied: ‘/scratch/fmriprep_wf/index.html’
Sentry is attempting to send 1 pending error messages
Waiting up to 10 seconds