Are you sure that spmregister is completing successfully? It is a little tricky to get spm set up properly, and I recently compounded the problem by changing the default intermediate file format to nifti (meaning that you needed spm5). I'm not sure what version you are using, but try looking at the terminal output for spm/matlab related errors.
Srihasam, Krishna wrote:
Hi,
I am having trouble overlaying my functional data generate by FSFAST stream onto the surfaces which I generated using Freesurfer. The registration is going haywire. I used spmregister-sess and the output registers coronal sections of the anatomical to horizontal sections of the fMRI data. So, I tried using the original anatomical image, not the surfaces I generated from it, the registration looks great. I used mri_info to check the difference between the images and my original anatomical image is 256x256x240 in size and its resolution is 0.5x0.5x0.5mm. The data seems to be stored as float. The brainmask.mgz in the mri directory of where I created the surfaces has different stats: 256x256x256 ; resolution: 1x1x1 and the data is in UCHAR. BTw, I am working on data from monkey rain. Any help will be more that appreciated..
-Krishna
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