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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