[Simnibs-discuss] hippocampal segmentation to stl

Axel Thielscher axelt at drcmr.dk
Fri Dec 11 21:39:43 CET 2020

Hi Ines,

when you open the nifti-file in freeview, is it then coregistered with 
the <subid>_T1fs_conform.nii.gz which headreco creates? If not, you can 
first run freesurfer and use the T1 and T2 which freesurfer stores as 
input to headreco.

You can then try the nii2msh tool, which puts the data from niftis into 
the mesh.

Let us know in case you get stuck.

Best regards,


On 12/9/2020 6:40 PM, Inês Violante wrote:
> Hello,
> I’ve just tried headreco and it is really cool.
> I would like to have a segmentation of the hippocampus in the same 
> space as the meshes generated by headreco.
> I have the hippocampus segmentation from freesurfer aligned to the 
> subject space. This is a .nii.gz file
> How can I now convert this to stl and have it in  the same space as 
> the other meshes generated by headreco?
> Thank you in advance!
> All the best,
> ines
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> Simnibs-discuss at drcmr.dk
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Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby

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