Thanks for the response,

Sorry, I can't seem to find a README file in that link?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] 7T submillimeter resolution processing

Hi Victor, it might make more sense to use the hires patch that we just developed last fall https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_6.0.0-2Dpatch_hcp_&d=DwMGaQ&c=WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0&m=zZ8Opj59_GKm7Ygk1kRWTa7DmrJ6DrH8JHOhPuuGmEU&s=BVaX5uxUce2TS3CoQwtX2itHqwTSSG0nhnBVKS8kqLM&e= there is a README file there with instructions on how to install and use

On 5/10/2019 11:18 AM, Zeng,Victor (BIDMC - Psychiatry) wrote:

Hi all,

I have a 7T dataset that I would like to have assistance in running FS6.0 for, and I have used this page as a reference: https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterReconhttps://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SubmillimeterRecon&d=DwMGaQ&c=WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0&m=zZ8Opj59_GKm7Ygk1kRWTa7DmrJ6DrH8JHOhPuuGmEU&s=p02Zrny_7vUXzS_Lj_tn_NWIkh7ZRaVz5ahPmVtBEgA&e=

I have some questions about the recon-all command, namely what the $IMAGE variable actually means. Also I have the $EXPERT_FILE as a txt file that just says:

mris_inflate -n 100?. That is fine as well, right?

Also I would like to know if the hippocampal/amyg nuc subfield parcellations is designed for 7T usage (In our neuroimaging lab, we've been using it for both 1.5T and 3T).

Thanks for your help.

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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