Dear Casey,
We don’t really have an easy way to work with meshes, so please understand that the support we can provide is limited.
But if you’re feeling very adventurous: before running segmentHA_T1.sh, set the environment variable WRITE_MESHES to 1, and you’ll get three new files per hemisphere:
?h.hippoAmygMesh-T1.v21.txt.gz: deformed mesh in image space
?'h.hippoAmygMeshAtlasSpace-T1.v21.txt.gz:deformed mesh in canonical space (in case you want to do some statistics)
?h.imageForMesh-T1.v21.mgz: corresponding image patch
The mesh files are compressed plain text files. The first part of the file gives you the x,y,z positions for the vertices, for a number of “positions”. You are interested in position 0; please disregard all other positions.
The second part of the file gives you the topology. And the third part gives you the probability vector associated with each vertex (for the prior, no the posterior).
Have a great rest of the weekend,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Casey Paquola <casey.paquola@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, March 22, 2020 at 12:45
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Surface meshes of hippocampal subfields
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Dear Freesurfer experts.
Is it possible to retrieve the mesh representations of the hippocampal subfields using the latest 7.0 development version of segmentHA_T1.sh?
I noticed that the meshes are saved as .txt files in the tmp directiory (following https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
Is it possible to keep these output files? Also, what format are meshes in within the txt file?
Many thanks,
Casey