Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Not yet, sorry. But it’s on my todo list. Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Jul 2016, at 14:39, Hibert, Matthew Louis > wrote: Hi

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Have you had a chance to look into the possibility of combining the -hires flag with the hippocampal subfield segmentation? Thanks, Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias,

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi all, I'll give some feedback about the two methods you've mentioned. I also tried using a 0.5 T1 image and then: *Changing the headers of the T1 and T2 images:* It worked for the 0.7mm T1, however, in the 0.5mm the tailarach aligment failed. In both cases I had the warning

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Matt, Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t crash when you run it! That said, I need to go through the code, and make sure that data are handled the way they are supposed to: the fact that it doesn’t crash doesn’t directly imply that it is working

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Would it also be possible to use the -hires flag in the initial recon-all command to prevent the T1 from being downsampled and maintain the voxel size that the T1 was acquired at, and use that resulting recon for the hippocampal subfield segmentation? I've tested this with MEMPRAGE

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Did you already do this? If so, a published reference would be more useful to me than instructions for how to do it, as I¹m more interested in making an argument for an acquisition protocol modification. Matt. From: on behalf of "Iglesias,

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Matt, you can use strategy 3 of my previous email ;-) Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 9 Jun 2016, at 19:31, Matt Glasser > wrote: I

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Fernando, Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to take advantage of multiple images with higher resolution, but it hasn’t been thoroughly tested and it’s not publicly

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

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] 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