I have been trying to use FreeSurfer on an aging population and running into difficulties with Talairach Registration. I am able to run the demonstrate date, but when I run my own data I am getting some very weird results. I have attached screenshots of the different planes for one subject. I have tried this with 5 subjects and getting the same kind of results.
In terms of scripting: I tried to run autorecon1 first and it failed with this error: ERROR: input(s) cannot have multiple frames!
setenv SUBJECTS_DIR test/DTI
recon-all -i DTI/00001.dcm -subjid again
cd $SUBJECTS_DIR/again/mri/orig
mv 001.mgz multiframe.mgz
mri_convert -nth 0 multiframe.mgz 001.mgz
recon-all -motioncor -subjid again
recon-all -talairach -subjid again
recon-all -nuintensitycor -subjid again
recon-all -normalization -subjid again
recon-all -skullstrip -subjid again
% checking registration
tkregister2 --mgz --s again --fstal
If anyone can provide some insight in terms of what I am doing wrong or how to fix the registration would be greatly appreciated.
Thank you,
Cherise.