Summary of what happened:
Hi everyone ! I have a longitudinal dataset and I am trying to add a flag --bids-filter-file on the fmriprep command in order for it to run separately my sessions.
Anybody has an idea ? 
thanks
Command used:
#!/bin/bash
for subj in `cat /data/qnilab/MSalavrakos/alcohol_T1s_subjectlist.txt`; do
micc_fmriprep --bidsdir /data/qnilab/MSalavrakos/Bids_MS --participant $subj --freesurfer --fmriprep-version 20.2.7 --ncpus 4 --output-spaces MNI152NLin6Asym:res-2 anat fsaverage --ramsize 16 --skip-bids-validation --outputdir /data/qnilab/MSalavrakos/fmriprep_output_MS_longitudinal_2 --force-workdir /data/qnilab/MSalavrakos/fmriprep_output_MS_longitudinal_2/work --bids-filter-file /data/qnilab/MSalavrakos/Bids_MS/file_filter_2.json
done
Version:
fMRIPrep-20.2.7
Environment (Docker, Singularity / Apptainer, custom installation):
???
Relevant log outputs (up to 20 lines):
I get this error message for every subject (this one below is the error message for sub 046, but it’s the same for all participants), even though they all have T1w images for the first session at least. And the original pipeline without the flag was running just fine
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/workflow.py", line 82, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 64, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 170, in init_single_subject_wf
"All workflows require T1w images.".format(subject_id))
Exception: No T1w images found for participant 046. All workflows require T1w images.
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
