Task Processing after fMRIPrep

I am modifying the following pipeline to process my task data preprocessed using fmriprep: Task fMRI Analysis using FSL and data preprocessed with fMRIPrep | Zenodo

I am running into an issue with the prepped_bold = layout.get(**query) line.

First, I get the following ValueError: ValueError: 'desc' is not a recognized entity. If you're sure you want to impose this constraint, set invalid_filters='allow'.

This is odd, considering desc- is a field output by fmriprep output, and a field that is specified in this pipeline, so I am pretty sure it is BIDS-valid. When I take the error message’s advice and include invalid_filters='allow', layout doesn’t find the image.

The file I am trying to process is named as follows: sub-MWMH378_ses-1_task-avoid_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz

And query is as follows: {'domains': 'derivatives', 'desc': 'preproc', 'suffix': 'bold', 'extensions': ['.nii', '.nii.gz'], 'subject': 'MWMH378', 'session': '1', 'task': 'avoid', 'space': 'MNI152NLin6Asym'}.

Any advice?

Hi, not a direct answer to this question, but you may find FitLins software (FitLins - Fitting Linear Models to BIDS Datasets — FitLins documentation) to be helpful. It was developed by some fMRIPrep devs to run linear models on fMRIPrep derivatives.

Ah! Amazing. This is just the sort of thing I was looking for. Thank you!