On Fri, Feb 4, 2011 at 10:30 AM, Katie Bettencourt <kcb@wjh.harvard.edu> wrote:

Can you tell me how to check that because I"m having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it.

Katie

On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang <yuhong.jiang@gmail.com> wrote:

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.com> wrote:

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

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Yuhong Vanessa Jiang, PhD,
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