but why not just load the aseg.mgz or whatever volume you are using directly into matlab? Then each structure has a different index that you can extract with the find command

cheers
Bruce
On Tue, 19 Jul 2016, Abbie McNulty wrote:

I attached the page in the last message, maybe it didn't show. I guess they aren't called segmentations, but
isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes
This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a .vtk file, I am not
converting anything

Abbie 

On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      Hi Abbie

      I'm not sure what page you mean. The segmentations start life as an .mgz file, so why convert them at all? Just load the aseg.mgz (or whichever
      segmentation you are interested in) into matlab directly

      cheers
      Bruce


      On Tue, 19 Jul 2016, Abbie McNulty wrote:

            Hi Bruce,
            So when I'm at this page, I am separating the different parts of the brain so that in the 3D view they show up as their own entity,
            and I am trying to
            individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file, which makes
            it difficult to upload
            into matlab. Is there a way to convert this 3D brain piece as an .mgz file?

            Thanks

            On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
            What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz


            Cheers
            Bruce


            On Jul 18, 2016, at 1:19 PM, Abbie McNulty <amcnult1@stanford.edu> wrote:

                  So we were able to figure out how to segment the different parts of the brain using the bert sample, but have run into another
            problem. 
            I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume
            segment
            saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can
            import it
            into matlab?

            Thanks!

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