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BBillot / hypothalamus_seg

a tool to segment the hypothalamus and associated subunits on T1-weighted MRI scans
Apache License 2.0
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Which mgz file I choose in the output of Freesurfer? #5

Closed enjoy-our-life closed 2 years ago

enjoy-our-life commented 2 years ago

Hi, In the output of Freesurfer/mri, Which .mgz file is the input file for this program I want to choose？ Thank you for your answer.

BBillot commented 2 years ago

I recommend to use nu.mgz.

With that being said, this tool is also available with FreeSurfer >= 7.1: https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits

If you're using FreeSurfer processed images, I would highly suggest that you use the FreeSurfer implementation of this tool. It's also super easy to use (nearly the same command as the github version). It just assumes you have run recon-all on your subjects, and at this point it will automatically select the nu.mgz file for you.

Hope this helps, Benjamin