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: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Iglesias, Eugenio" <e.igles...@ucl.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, June 9, 2016 at 1:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: 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 <m...@ma-tea.com> wrote: > > 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. > _______________________________________________ > 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. _______________________________________________ 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.
_______________________________________________ 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.
