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You definitely want 3D sequences for FreeSurfer. These can be T1w, T2w, or FLAIR.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Georgia Kapizioni <geo.kapizioni@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, January 5, 2021 at 5:37 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Correcting pial surface with Flair sequence
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Hello Freesurfer Developers,
I am conducting a group analysis between a patients and a control group. I have accomplished recon-all individual analysis and I want to correct pial surface using 3D Flair.
I would like to ask two specific things:
1. Is 3D Flair appropriate or only T2 Flair is recommended for such correction. From what I have read on previous posts, it is usually recommended to use T2 Flair.
2. For my data, for most of my 3D data slice thickness is 1 mm, but for some of them is 1.48 mm. Is that difference going to affect analysis results?
Thank you in advance,
Georgia
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