Can you send the commands you used to check the registration ? On 9/16/20 2:24 PM, Wenzhen Zhao wrote: > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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