External Email - Use Caution

Dear Eugenio,

Thank you for quick response. That will be great if we could achieve it with whole-head segmentation too, considering its shorter run time, but can understand that it could be less reliable. If implemented, is it something that will be included as a patch to current release or will it part of next big release?

Thank you, Sneha

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Tuesday, May 5, 2020 11:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields

Dear Sneha, We use cortical and white matter parcels in the hippocampal subfields, which is more reliable than using the whole white / gray matter to compute parameters. But it could be hacked, albeit it would be a bit less reliable. I’ll add this to the wishlist / to-do list (unfortunately it isn’t likely I’ll be able to look at it any time soon…) Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.comhttps://urldefense.proofpoint.com/v2/url?u=http-3A__www.jeiglesias.com&d=DwMGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=nvkbJLwGOMiMASjTHtMkLyhmC8Acu6t2DmhnDK56BfY&s=Jzs0r2z0IWEF_kMnRWpLOUDfJdqkszjHdQCQKVvAnfs&e=

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2003@med.cornell.edumailto:snp2003@med.cornell.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, May 5, 2020 at 10:46 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] samseg with subfields

External Email - Use Caution Dear experts,

I want to revisit if anyone has ran subfield analysis just by running samseg? If it is possible is it as reliable as from running regular routine with “-all” recon-all flag?

Thank you,

Sneha

From: Sneha Pandya Sent: Thursday, April 30, 2020 4:15 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, amygdalar, thalamic nuclei, and brainstem structures) when we only run samseg on our dataset?

Thank you, Sneha