Neurodevelopmental sample freesurfer reconall - need each session processed separately

Software Support
1

Hi,

I wonder if someone from fMRIprep could clarify how we are running our processing. We have a neurodevelopmental sample of participants which we are following up with an MRI scan every year. We are processing all the MRI scans as they come in and data collection is ongoing. We elected to run a bidsfilter to point to each session specific anatomic file and functional file because we wanted each session to be treated separately (we hypothesized that there would be differences in structural scans over the year). We didn’t want to use the longitudinal flag which averages the anatomic scans over sessions because a) we wanted treated separately b) not all the scans have been collected (some participants would have 3 sessions while others 2).

Everything has been going really well EXCEPT at follow up sessions, we are not seeing a separate freesurfer file. I am guessing this is because it’s NOT rerun recon all on the follow up session and just using the baseline.

Questions…

  1. Am I correct about this? Given our hypothesize, should we be concerned for functional preprocessing? I am pretty certain we will need to rerun the follow-up anatomic processing regardless.

  2. Is there any way to set this so that it treats each session completely separate for anatomic processing outside of creating completely separate BIDS folders for baseline and follow-up? We have a very large dataset and will have several follow up sessions and want to try to keep things as organized as possible, worried separate session specific BIDS folders is going to get messy.

Thanks for any assistance you can provide,

Jennifer

2

Hi @AustinBipolar,

For this we’d need to see the code and some file organization. If you specify a fs-subjects-dir in which a subject folder already exists, recon-all will be skipped and the pre-existing outputs will be used. You might be well served renaming freesurfer subject directories after running, or putting them in session specific folders (e.g., freesurfer_ses-1/sub-XX or freesurfer/ses-XX_ses-1).

Yes, even if you are not using CIFTI data, I imagine it is bad if boundary based registration (from freesurfer) is being run on a T1w that was not used to generate the freesurfer data.

BIDS filter files should do the trick, with careful specifying/naming of FreeSurfer ingressing. If you want to be extra careful, you can make temporary BIDS directories with single sessions in temporary/scratch space.

Best,
Steven