Dear Arsenije

The atlas is encoded in a tetrahedral mesh, so there is no nifti file for it.

Having said that, it is possible to rasterize the atlas at a target resolution.

The command is the following:

kvlRasterizeAtlasMesh $FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz  $FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz X  -1

where X is the label number (see $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt for a listing; 0 is cortex, 1 is cerebral white matter, etc). -1 indicates the reference position of the atlas, so do not modify that.

This command will create a file called rasterized.mgz. You can convert it to nifty with mri_convert, eg.

mri_convert rasterized.mgz probability_label_X.nii.gz

You can do this with all the different hippocampal labels. And if you want a probability for the whole hippocampus, which is probably what you need for the registration with your manual mask, you can sum the probabilities of the different subfields into a single volume (e.g., with fslmaths)

I hope this helps,

/Eugenio

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Arsenije Subotic <arsenije.subotic1@ucalgary.ca>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 22 March 2018 at 15:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfields

Hi all

I would like to use subfield specific hippocampus maps that were produced Dr Iglesias's Lab: https://sites.google.com/site/jeiglesias/hippocampal-subfields

These maps are available via FreeSurfer, however our lab is trying to segment hippocampus subregions from already manually extracted hippocampuses. In other words, we have manually traced hippocampus masks in a NIFTI format that we would like to co-register with these maps. 

How can I directly download subfield specific hippocampal atlases in a NIFTI format so that we can use non linear co registration after?

Thank you very much.

Look forward hearing from you,

Arsenije