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