For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you want a particular GM or all GM?

Ed Gronenschild wrote:

Doug,

The file "segmentation.mgz" doesn't exist. I think that you mean that segmentation.mgz stands for either WM or GM. Can you provide me the exact file names of the final WM and GM segmentations.

Ed

On 25 Aug 2009, at 17:28, Douglas N Greve wrote:

...

mri_convert segmentation.mgz segmentation.nii

should do it

doug

Ed Gronenschild wrote:

...

Hi,

I would like to extract the WM and GM segmentations used for the final cortical thickness calculations as nifti files. How can I do that?

Ed

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