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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: image.png]
External Email - Use Caution
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: image.png]
External Email - Use Caution
Can you send a snapshot in the coronal plane?
On 6/20/2023 8:20 AM, Michael Mc Laughlin wrote:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1B0rI_XlWlVKSDCNvBgnidZNZC5QrkEvkRzhua99Gc7XvZ6...
External Email - Use Caution
Here is a coronal view.
[image: image.png]
On Tue, Jun 20, 2023 at 3:01 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use CautionCan you send a snapshot in the coronal plane?
On 6/20/2023 8:20 AM, Michael Mc Laughlin wrote:
External Email - Use CautionHow 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: image.png]
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/12Sc79yeq5eqsfFVn7pv2hjj-uAqmIxEc9Nm5Wncr99CLFi... https://secure-web.cisco.com/1B0rI_XlWlVKSDCNvBgnidZNZC5QrkEvkRzhua99Gc7XvZ6JM-d0S-gg-4laIKAdyeHUpc5PU651Eb8TAfbFyUj6Bk8FKpJEZTqituKzSn8YLMT5ErTeOWBki93zD3CJ4Lfdk9bn4zTJ47qSUaDFaZzM3xkzEMTM5gR8pXhFupfBBzbAf8okE9kl3HcPs9R9oq5oE2Hv3DfmzOAejvDjkdfcFp5wzC3Y92nA8uT48k2BnXRumuuSspu6JZ2fAcfvw5Geq_MX4dwj4BVDnUYVq5A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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: image.png]
On Tue, Jun 20, 2023 at 3:01 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use CautionCan you send a snapshot in the coronal plane?
On 6/20/2023 8:20 AM, Michael Mc Laughlin wrote:
External Email - Use CautionHow 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: image.png]
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Michael Mc Laughlin