I edited the white matter, and then ran recon-all command. The image I included shows that the white matter changes, but the contour lines have not changed. Subsequently, how do I change the contour lines to reflect the changes I made to the white matter. Additionally, is changing the control points the way to change grey matter?

Thanks,

Gaurang

On 5/17/16, 5:44 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Gaurang

what volume are you editing? You should be editing the wm.mgz.

cheers Bruce

On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote:

...

This is how the white matter changes look like after making corrections and running recon all.

From: "Limachia , Gaurang (NIH/NINDS) [F]" gaurang.limachia@nih.gov Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, May 17, 2016 at 4:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer

I made the necessary changes to the white matter, and when I ran recon all the changes with the voxels showed up, but there was no change to the contour lines. In order to change the gray matter volume, I can¹t find the changes I already made on the white matter (the picture with green control points). If I am able to see the changes I made to the white matter, I can utilize the control points to modify the segmentation. Also will this impact the gray matter volume as well as per your previous response to my question.

Thanks,

Gaurang

Dr. Fischl,

I loaded the t1 file from our patient dataset freesurfer>t1>mri>wm.mgz. When I was editing the white matter, I had the wm highlighted, and not brainmask under the volumes.

Best, Gaurang

On 5/17/16, 5:56 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Gaurang

it looks like you edited the white matter, but not in the wm.mgz, which is what we require. What volume (i.e. what was the name of the file you loaded) did you edit?

cheers Bruce On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote:

...

I edited the white matter, and then ran recon-all command. The image I included shows that the white matter changes, but the contour lines have not changed. Subsequently, how do I change the contour lines to reflect the changes I made to the white matter. Additionally, is changing the control points the way to change grey matter?

Thanks,

Gaurang

On 5/17/16, 5:44 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Hi Gaurang

what volume are you editing? You should be editing the wm.mgz.

cheers Bruce

On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote:

...

This is how the white matter changes look like after making corrections and running recon all.

From: "Limachia , Gaurang (NIH/NINDS) [F]" gaurang.limachia@nih.gov Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, May 17, 2016 at 4:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer

I made the necessary changes to the white matter, and when I ran recon all the changes with the voxels showed up, but there was no change to the contour lines. In order to change the gray matter volume, I can¹t find the changes I already made on the white matter (the picture with green control points). If I am able to see the changes I made to the white matter, I can utilize the control points to modify the segmentation. Also will this impact the gray matter volume as well as per your previous response to my question.

Thanks,

Gaurang

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