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The "brainstem pipeline" described here:

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

Thanks!
-Dan

On Wed, 30 May 2018, Bruce Fischl wrote:

> Hi Dan
>
> which brainstem atlas do you mean?
>
> cheers
> Bruce
>
>
> On Wed, 30 May 2018,
> djpeters@u.washington.edu wrote:
>
>>        External Email - Use Caution
>>
>> Hi Freesurfer email list,
>>
>>   I'm trying to get the midbrain mask from the brainstem segmentation
>>   pipeline into standard space, for use in analyzing some data in other
>>   modalities. I have labeled T1s in individual-space (it's a longitudinal
>>   pipeline). Does the brainstem atlas already exist somewhere in
>>   MNI-space as a mask? If so, where could I find it? I've found the ROI
>>   mesh data, but I don't know how to convert that into a voxel mask.
>>
>> Thanks so much,
>> -Dan Peterson
>>
>>
>>
>>
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