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Hi Douglas,

I think I found the problem. After running recon-all on the T1-MPRAGE mri scan I ran  recon-all with a T2 scan with the flags -T2 -autorecon3 -T2pial and this updated the results. The resolution of the T2 mri I used was only 4.8mm in the Z-direction and this appears to have screwed up the results. When I ran recon-all in a fresh subject directory the results looked much better.

Michael


On Tue, Jun 20, 2023 at 3:21 PM Michael Mc Laughlin <michael@thecurate.com> wrote:

Here is a coronal view.

image.png

On Tue, Jun 20, 2023 at 3:01 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

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Can you send a snapshot in the coronal plane?

On 6/20/2023 8:20 AM, Michael Mc Laughlin wrote:

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How can I set the threshold used for Gray matter?

I have a T1 mprage scan and a large amount of gray matter is clearly not being included (see attached). There is a lot of help on setting the GM/WM threshold but I can't find anything about setting the GM/CSF threshold.

image.png


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