Trying to use the new --bids-filter-file
to select only the first session to process for a given participant. I finally figured out the config.json
file (documentation/examples on this that aren’t buried in PRs leave a bit to be desired, I will try to add one when I’m sure it works). I know that this participant starts running without errors using 20.0.2
without a filtering file. However, when I try to add the filter, I get the error below:
Running fMRIPREP version 20.0.2:
* BIDS dataset path: /mnt.
* Participant list: ['CBPD0207'].
* Run identifier: 20200309-183330_24bf583e-e89a-4cb4-ab9c-097ee54a7a3c.
Spatial References:
- Reference(space='MNI152NLin6Asym', spec={})
- Reference(space='T1w', spec={})
- Reference(space='MNIPediatricAsym', spec={'res': '1', 'cohort': '2'})
200309-18:35:48,207 nipype.utils INFO:
No new version available.
Process Process-2:
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/run.py", line 691, in build_workflow
bids_filters=bids_filters,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 274, in init_fmriprep_wf
bids_filters=bids_filters,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 499, in init_single_subject_wf
subject_id, task_id if task_id else '<all>'))
Exception: No BOLD images found for participant CBPD0207 and task <all>. All workflows require BOLD images.
Config file:
{
"t1w": {
"datatype": "anat",
"session": "1",
"suffix": "T1w"
},
"bold": {
"datatype": "func",
"session": "1",
"suffix": "bold"
}
}
It looks like <all>
is not being evaluated properly? Or…something with the config file, I’m still confused about how to set it up properly.