Hi All,

I'm running FS v. 5.3 on Gentoo Linux.

I made a study, where all subjects during one session had T1, resting-state and task-based fMRI. I processed all anatomical data through standard recon-all (it worked well), and the task-based fMRI through FS-FAST - which also generated fine results.

Now I wanted to look into the rs-fMRI with functional connectivity. I made a separate directory tree for this purpose (in order not to mess task and rest data), and unfortunately the bbregister doesn't handle the registration during preproc-sess properly. Misalignment is big and covers all runs. BBR-sums of all of participants (N=39) exceed 0.8 (some of them exceed 1.0). What's interesting is that bbregister previously managed the task-based fMRI data well (with no BBR-sum exceeding 0.8). I double checked the data for any i.e. conversion/orientation faults, but found none.

The command for preprocessing was identical in rs-fMRI and task-based fMRI:
preproc-sess -sf <sessid> -d <ProjectDirectory> -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -fsd bold

I attach exemplary register log file from rs-fMRI subject registration (BBRsum=0.9704). This subject's task-based fMRI BBR-sum was 0.55.

My question is - what may be the cause of such a discrepancy between registration of two functional runs taken one by one (the rs-fMRI preceded the task based)? Does anyone have an idea how to fix the problem?

Best regards,

Patrycja