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
