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-boun...@nmr.mgh.harvard.edu> on behalf of Arsenije Subotic <arsenije.subot...@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.