Hello:

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!

I changed the script and did the following (running one line at a time):

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.

Cherise R. Chin Fatt; MSc
Doctoral Student in Cognition and Neuroscience
School of Behavioral and Brain Sciences
The University of Texas at Dallas