I would be interested to know how well 0.7mm isotropic resolution data performs at hippocampal segmentation. It would be better if folks could do this then needing to acquire specialized anisotropic scans for hippocampal segmentation.
Peace, Matt. From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fernando Pasquini Santos <fernandop...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, June 9, 2016 at 1:23 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input? Dear, I have a doubt regarding the input T1 image used for the Hippocampal Subfield segmentation in Freesurfer 6.0 - https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields In this documentation it says that I can use a standard 1mm T1 image or the same standard 1mm T1 image with an additional scan. However, I want to use a 0.7mm T1 image as input, with an additional T2 scan. When I run the program with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel size. So, I don't know if this happens just because of the recon-all program or if the segmentation is being done in the downsampled T1 image or in the original 0.7mm. By reading the article "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI" I saw that, in the methods section, the algorithm is used to segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? Obviously, doing the segmentation directly on 0.7mm data would be better than a downsampled version to 1mm... Thanks, Fernando Pasquini Santos PhD student in Dynamic Systems fernandosan...@pitt.edu fernando.pasquini.san...@usp.br _______________________________________________ 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.
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