Sorry I forgot to attach the following link of previous post I referred to regarding the same issue: here it is:https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1408&L=spm&P=R24941&1=spm&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
Dear John and others,
I have some errors using the new segmentation parameters on SPM 12 to acquire the normalisation parameters for my functional data.
Using the new segmentation on SPM 12, I generated iy*.nii and y*.nii images, which I presumed that these images contained information regarding the normalisation (y*.nii for normalising images from native to MNI space). I input the y*.nii image for normalising the structural and functional images. When I compare the structural image to a template T1 image, it looked fine. However, I noticed that at least one of my subjects, the functional images did not normalise to MNI space properly, specifically, the functional brain image looks bigger than the T1 image brain, although I think they should correspond to each other when I display them together. Also, when I looked at the T-contrasts of that particular subject, there were activations outside the brain. I think it's most likely an issue of the skull, thus, it would be better if I skull stripped the structural image before I start the segmentation process for normalisation purposes.
My question is, whether or not to skull strip the structural image did not affect the normalisation process in the previous versions of SPM, why is this affecting the normalisation process in the new version? Also, the procedure that I described above, is that correct?
Is there a way include skull stripping algorithms before the segmentation process?
Thank you.
Kind regards,
Hweeling
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Dear SPM experts,
I followed exactly the same procedure for segmentation and I am facing exactly the same issue- having activations little bit outside the brain. The functional brain image looks bigger than the T1 image brain. Could you please confirm if the procedure Hweeling described is correct, why there are activations outside the brain and how can we avoid that ?
Thanks,
Sahil
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