Do you know why it has multiple frames? What kind of image is it?
On Apr 3, 2013, at 10:51 PM, "Cherise R. Chin Fatt" cherise.chinfatt@utdallas.edu wrote:
Hello Bruce:
I am using a T1-weighted image.
On Wed, Apr 3, 2013 at 9:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Ae you trying to put a diffusion scan through recon-all? That won't work, it needs to be T1 weighted Bruce
On Apr 3, 2013, at 10:23 PM, "Cherise R. Chin Fatt" <cherise.chinfatt@utdallas.edumailto:cherise.chinfatt@utdallas.edu> wrote:
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 <Screen Shot 2013-04-03 at 8.39.26 PM.png> <Screen Shot 2013-04-03 at 8.39.40 PM.png> <Screen Shot 2013-04-03 at 8.39.54 PM.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Cherise R. Chin Fatt; MSc Doctoral Student in Cognition and Neuroscience School of Behavioral and Brain Sciences The University of Texas at Dallas