I need to run freesurfer 7.1.1 on my mri data, therefore I will need to run FreeSurfer outside of fmriprep.
I have longitudinal data that is approximately 1 year apart for each timepoint. In order to make the FreeSurfer results compatible with fmriprep, how should I run the recon-all command? Comments from previous threads seem somewhat inconclusive.
I was thinking of merging the two T1w images together and running freesurfer on the combined T1, though this may not be ideal, since I would want separate structural measures for each timepoint.
The proper procedure is largely dependent on your analytical goals.
Do you want a single template made across all time points? If so, you can use the longitudinal stream in FreeSurfer FsTutorial/LongitudinalTutorial - Free Surfer Wiki. Put the combined template recon-all output into a folder like bids/derivatives/freesurfer_long/sub-xxx, and then pass bids/derivatives/freesurfer_long in the --fs-subjects-dir fmriprep argument.
If you want to keep the time points separate (which hinders the ability to longitudinal analyses but might be warranted if the T1s have drastically different shapes or are very far apart in time) then you should run recon-all separately for each T1, putting outputs into different folders, e.g., bids/derivatives/freesurfer_T1/sub-xxx, bids/derivatives/freesurfer_T2/sub-xxx etc. Then set the --fs-subjects-dir in fMRIPrep to bids/derivatives/freesurfer_TX and use a --bids-filter-file to only analyze the data from the session you want to analyze. Loop across sessions.
Thank you very much for replying. Now I ran fmriprep with the --fs-no-reconall flag. I wanna ran freesurfer outside fmriprep and then link the output to fmriprep output. The fmriprep output has an merged T1 file across two sessions fmriprep/anat/*_desc-preproc_T1w.nii.gz. Is it the correct input for freesurfer?
No, raw T1s should be used for FreeSurfer. The fmriprep anatomical outputs are preprocessed. And fs-no-reconall is not recommended. It disables surface based algorithms for spatial normalization which tend to work better than volume-based methods.