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.
Hi Cherise, the multiple frame error hints to some issue with the data. It means that it has multiple images, like an fMRI volume (which will not work), but it could be multiecho mprage (which would be ok after computing RMS). What are you using as input? doug
On 4/3/13 10:23 PM, Cherise R. Chin Fatt 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Cherise R. Chin Fatt -
Douglas Greve