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