Hello FMRIprep experts,
I am running fmriprep Version: 1.5.0 installed with pip on a manually prepared environment
I am running a single participant analysis with the purpose of testing sdc with pepolar with the following command:
fmriprep mybids/ out/ participant --participant-label sub-01 --fs-no-reconall --omp-nthreads 4 --n_cpus 4 --ignore slicetiming --bold2t1w-dof 6 -w temp/ --output-spaces T1w
the dataset passed the BIDS validation step (it’s just T1W, BOLD AP, BOLD AP) and process through the workflows until I reach :
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask”.
Traceback (most recent call last):
File “/home/miniconda3/envs/fmriprep/bin/fmriprep”, line 10, in
sys.exit(main())
File “/home/miniconda3/envs/fmriprep/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 457, in main
check_call(cmd, timeout=10)
File “/home/miniconda3/envs/fmriprep/lib/python3.7/subprocess.py”, line 342, in check_call
retcode = call(*popenargs, **kwargs)
File “/home/miniconda3/envs/fmriprep/lib/python3.7/subprocess.py”, line 323, in call
with Popen(*popenargs, **kwargs) as p:
File “/home/miniconda3/envs/fmriprep/lib/python3.7/site-packages/sentry_sdk/integrations/stdlib.py”, line 187, in sentry_patched_popen_init
return old_popen_init(self, *a, **kw)
File “/home/miniconda3/envs/fmriprep/lib/python3.7/subprocess.py”, line 775, in init
restore_signals, start_new_session)
File “/home/miniconda3/envs/fmriprep/lib/python3.7/subprocess.py”, line 1522, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: ‘pandoc’
Any advice on this?
Thanks,
Marcello