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These outputs were generated using the regular pipeline 7.1.1

I tried the infant pipeline as well but results were less desirable.

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________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Wednesday, October 21, 2020, 10:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer edits

* External Email - Caution * Hi Jim, Did you use the infant or the regular pipeline here? Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Tuesday, October 20, 2020 11:24 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer edits

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Hi freesurfer editing experts.

Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run through FS 7.1.1

I’m hoping for feedback on the best way to make the relevant edits to the three blue-circled regions.

1. In the superior regions I think control points will help to pick up some WM to help fuill

2. In the left hemisphere medial prefrontal (gyrus rectus) regions, the WM is overestimated. I presume removing WM voxels from the wm.mgz is the best approach?

3. The left temporal pole region is missing GM/cortex and there really isn’t any WM that would help with controls points or adding WM voxels. How can I add GM to this area?

[cid:image007.jpg@01D6A6CB.3399D5E0][cid:image008.jpg@01D6A6CB.3399D5E0]

[cid:image009.jpg@01D6A6CB.3399D5E0][cid:image010.jpg@01D6A6CB.3399D5E0]

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It looks like the image darkens a lot at the top. Try putting control points in the WWM near the start of the gyrus. make sure they are truly in WM!

On 10/25/2020 9:03 PM, Alexopoulos, Dimitrios wrote:

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Any comments from FS users to best best tackle these manual edits?

Jim

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu *Sent:* Tuesday, October 20, 2020, 10:25 AM *To:* Freesurfer support list *Subject:* [Freesurfer] Freesurfer edits

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Hi freesurfer editing experts.

Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run through FS 7.1.1

I’m hoping for feedback on the best way to make the relevant edits to the three blue-circled regions.

1.In the superior regions I think control points will help to pick up some WM to help fuill

2.In the left hemisphere medial prefrontal (gyrus rectus) regions, the WM is overestimated. I presume removing WM voxels from the wm.mgz is the best approach?

3.The left temporal pole region is missing GM/cortex and there really isn’t any WM that would help with controls points or adding WM voxels. How can I add GM to this area?

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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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