External Email - Use Caution
Dear freesurfer developers,
I am working on preprocessing resting state fMRI and used the following command.
$ preproc-sess -s sess01 -fsd rest -stc siemens -surface fsaverage lhrh -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-session
When I tried to visualize f.nii.gz with registration file applied and overlaid with aparc+aseg.mgz from structural analysis, they do not overlap. It seems like the orientation is not the same, and the f.nii.gz with registration seems to be 90 degree rotated from apjarc+ aseg. mgz. (I wish I could attach a screenshot, but last time I tried, it says my email exceeded the capacity and sent to the moderator)
I also tried bbregister. I was suggested not to use —init-rr, so I tried all the other registration methods, but same problem occurs.
$bbregister --mov sess01/rest/001/template.nii.gz --t2 --s subject --lta register.dof6.lta
—init-rr does a good job when I checked visually by applying registration on f.nii.gz and checked if it overlaps with structural scan. But, I thought the registration file goes both ways, but when I checked structural scan (orig.mgz or aparc+aseg.mgz) with registration file and overlapped with functional scan (f.nii.gz), it does not overlap.
Is there a specific way that I have to apply a registration file to visualize the transformation in the opposite direction? If preprocess registration does not work, is there any other method that I can try to make them aligned?
Thank you for your time and help !
Best, Wenzhen