Hi Maryam,
You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical.
-Yuhong
On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam mvaziri.p@gmail.comwrote:
Hi,
I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed.
I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ):
path(path,'/Applications/spm8');
I run preprocessing on the data using the following command:
preproc-sess -nosmooth -sf retino-sess -df retino.dir
then I run automatic registration with the following command:
spmregister-sess -sf retino-sess -df retino.dir
It runs smoothly and there seems to be no errors. But when I try to check the registration with this command:
tkregister-sess -sf retino-sess -df retino.dir -inorm
what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter.
Thanks,
Maryam
Freesurfer mailing list 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.