Hi everyone,
I’ve been running into some unfamiliar issues with the previous two versions of fmriprep (the current one 20.2.0 and 20.2.1) where for some subjects their json files have “null” values in their confound estimates (see attached). With each of these versions it happens to a different set of subjects, making it a little challenging to troubleshoot. I did check these subjects anat folders and they have other tissue segmentations (e.g., can visualized wm and csf segmentations), so I don’t think it’s a freesurfer issue. This didn’t happen with version 1.5.1, but I know there were other bugs with that one, so I wanted to use the most up to date version. I’m thinking because of our longitudinal BIDS structure, the parent anat folder may have files overwritten since the anatomical segmentations do not land in the anat folder of the session folders. The reason I’m thinking this is bc it seems to be only a ses-T1 issue (if it’s running longitudinally through anat processing first, then the files that land in the parent anat folder come from later session segmentations?). For example,
- sub-XXX
- anat (all the segmentation niftis and txt files, but “ses-T” is not in any file names, which makes me think that it’s overwritten?)
- log
- figures
- ses-T1
- anat (just the orig_to-T1w_mode-image_xfm.txt)
- func
- ses-T1x
- anat (just the orig_to-T1w_mode-image_xfm.txt)
- func
- ses-T2
- anat (just the orig_to-T1w_mode-image_xfm.txt)
- func
I’m testing out just one subject who has this structure and on only time one to see if the issue persists, but wanted to ask if anyone has run into this at any point or may have some troubleshooting advice.
Thank you so much!!
Jackie