Can you send the bbregister log file?
On 9/18/2020 12:02 PM, Wenzhen Zhao wrote:
External Email - Use CautionDear Douglas,
tkregisterfv --mov sess01/rest/template.nii.gz --targ subject/mri/orig.mgz --reg register.lta
This is the command that I used to check registration. I also checked them by opening Freeview and manually open the template.nii.gz with registration file, then overlaid it with orig.mgz to see if they overlap.
Best, Wenzhen
On Sep 18, 2020, at 10:57 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
Can you send the commands you used to check the registration ?
On 9/16/20 2:24 PM, Wenzhen Zhao wrote:
External Email - Use CautionDear 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
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