Dear Julian,
Apologies if your message feel in the cracks.
If you want to visualize the atlas, you can use a (very buggy) program called kvlViewMeshCollectionWithGUI.
First, source Freesurfer and cd into the following directory: cd $FREESURFER_HOME/average/hippoSF/atlas
Then, run the following command kvlViewMeshCollectionWithGUI AtlasMesh.gz
Once the GUI has opened, selected Mesh Number: Reference mesh.
Finally, check “show summary” to produce the color-coded image.
Cheers,
/Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 12 May 2017, at 20:43, Julian Jäckle <jaecklejulian@googlemail.commailto:jaecklejulian@googlemail.com> wrote:
Dear all I know that i’ve posted this question before, but yet nobody replied and we do really need an answer to close our project. Your “Segmentation of hippocampal subfields” wiki article refers to the publication: “A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI“. Within the paper there are two figures No. 4 & 6 demonstrating the probabilistic atlas and mesh deformation. We do need to know how you created these illustrations. I attached one of the images as an example Thanks a lot Julian
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