I want to use a T1w image preprocessed by QSIprep as an input T1w image for fmriprep, so that the derivatives of the two pipelines end up in the same space. I am trying to add the preprocessed T1w image as an additional acquisition in the input anat folder (so that my anat folder has two niftis: sub-xxx_ses-1_acq-qsiprep_T1w.nii.gz, sub-xxx_ses-1_acq-original_T1w.nii.gz). Then I am trying to use a bids-filter-file to select the acq-qsiprep one. My file looks like this:
The pipeline runs without any error but seems to ignore this file (I saw that this issue was previously raised here and here: --bids-filter-file seems not working as supposed · Issue #2368 · nipreps/fmriprep · GitHub ).
1- Is there a syntax error in my filter file? is there a documentation or example that i can follow to make sure I’m filtering properly?
2- My html log says that 2 T1w images were detected in the BIDS folder, but it’s unclear from the documentation which of them was used as the T1w reference for coregistration. After playing around and checking the output, it seems to me that fmriprep chooses the first T1w in the anat folder in an alphabetical order? meaning, when I had ‘acq-qsiprep’ compared with ‘acq-original’, the preprocessed functionals ended up in the same space as acq-original. But when I renamed ‘acq-original’ to ‘acq-z’,my derivatives ended up in the same space as ‘acq-qsiprep’… Can someone confirm if that’s the case?
Thanks in advance,