Hi,

I was wondering where I can find the hippocampus labels. See:  https://pubmed.ncbi.nlm.nih.gov/25585022...
I thought these were separate label files, but I am not sure if that is still the case.

Thanks,

Niels

Dear Niels,

The original delineations from Kjønigsen et al., representing version 2 of the atlas, are shared as a complete labeled volume of the brain, including both the detailed delineations of the hippocampal and parahippocampal regions, as well as all the other regions covering the rest of the brain (as in v1.01). Please see WHS_SD_rat_atlas_v2.nii.gz and WHS_SD_rat_atlas_v2.label under Downloads.

The label file is set up so that non-hippocampal regions are hidden in the 3D view in ITK-SnAP, in case you would like to generate meshes for a figure. In case you need a volume containing only the hippocampal regions, you can delete all the other labels via Segmentation -> Label editor, or by editing the label values in the NIfTI volume itself, for example using Convert3D (the command line companion to ITK-SnAP): https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md#-retain-labels-retain-labels-in-a-label-image

We can also generate and send you such an image if that would be of help.

Best regards,
Eszter