Perfect.
now if I wanted to use plotmesh with this, what would the variables be for
x and y: plotmesh('x,y')
On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
>
>
> [aseg,M,mr] = load_mgh('aseg.mgz');
> ind = find(aseg == 16);
>
>
> that will give you the indices in the aseg volume of the voxels that have
> the brainstem label (16). Then you can do what you want with it. The label
> came from $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>
> cheers
> Bruce
>
> On Tue, 19 Jul 2016, Abbie McNulty wrote:
>
> So say I load aseg.mgz into matlab and I want to extract the brainstem in
>> matlab to plot its own volumetric mesh vs. the entire brain, how would I
>> extract
>> the brainstem in matlab?
>>
>> On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> 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 <
>> fis...@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 <
>> fis...@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 <
>> amcnu...@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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>> B.A. Candidate in Bioengineering
>> Stanford Women's XC/ Track and Field
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>> Stanford University Class of 2018
>> B.A. Candidate in Bioengineering
>> Stanford Women's XC/ Track and Field
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>> Stanford University Class of 2018
>> B.A. Candidate in Bioengineering
>> Stanford Women's XC/ Track and Field
>>
>>
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--
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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