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Problems about CSF segmented in Freesurfer and MRI anatomy import

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Hi! I'm trying to do the image reconstruction using AtlasViewer, but found the reconstruction result obtained from my specific subject's MRI anatomy was quite different from what we expected, while the result from Colin is great. We assumed the problem is caused by the MRI anatomy import, because we used Freesurfer commend below to generate an 'ventricles.mgz' as the CSF import file. However, in freeview we found that the ventricles.mgz didn't contain the CSF between the skull and the brain, which may influence our image reconstruction result. So I'm now trying to ask you guys how you import your specific CSF anatomy files? Is the ventricles.mgz generated by Freesurfer fine or not? Or how to generate a CSF import from Freesurfer?

mri_binarize --i aparc+aseg.mgz --ventricles --o ventricles.mgz


Apart from the CSF, I'm also wondering can we just use the T1.mgz as the head file? Or should I segment a head file with the Freesurfer commend 'mri_seghead'?


Thanks in advance!