External Email - Use Caution        

Dear Dr. Nolan,

 

Thank you so much for your help; I really appreciate it.

 

I’m currently using a heat color map for brainmask.mgz and the grayscale color map for T1.mgz.

 

After shading (step 4), should I expect to see the newly cloned voxels (perhaps as red voxels added to brainmask.mgz) immediately? Or, nothing actually appears after shading and the cloned voxels added to brainmask.mgz only appear in brainmask.mgz after another run of recon-all?

 

Also, what do you mean by “Place the cursor in the voxels you have cloned to check the value is the same in both the target and reference volumes.”? What value?

 

 

Thank you so much!
Emily Harriott

 

 

From: Nolan, Jackson
Sent: Thursday, March 2, 2023 5:16 PM
To: Freesurfer support list
Cc: Harriott, Emily M
Subject: Re: [Freesurfer] more detailed instructions for cloning voxels & confirmation that the cloning worked

 

Hello Emily,

 

To clone voxels from your T1.mgz -> brainmask.mgz:

  1. select brainmask.mgz as your active volume
  2. click on 'Voxel Edit' -> 'Clone Voxel'
  3. set T1.mgz as the reference volume
  4. shade desired voxels to clone

I would recommend having your brainmask on top of the T1, as well as changing the opacity (and possibly the colormap) of the brainmask.

Place the cursor in the voxels you have cloned to check the value is the same in both the target and reference volumes.

 

Best,

Jackson

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Harriott, Emily M <emily.m.harriott@vanderbilt.edu>
Sent: Tuesday, February 28, 2023 5:47 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] more detailed instructions for cloning voxels & confirmation that the cloning worked

 

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Dear FS experts,

 

I hope this email finds you all doing well.

I am trying to clone voxels back into brainmask.mgz from T1.mgz, but am struggling. I am hoping one of the FS geniuses on here might be able to help me.

 

  1. How exactly do you do it (what do you click on and when, what images do you have active, and what settings are set in the GUI, etc.)?
    1. I read through MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/VoxelEdit but am not sure it worked so require more detailed instructions that I was unfortunately unable to find on the FreeSurfer website or via google.
  1. How do you tell if it worked? I saw MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56601.html this previous post but it does not seem to have been answered.

 

Any assistance would be greatly appreciated.

 

Thank you so much!

 

 

All the best,

Emily Harriott

PhD student, Vanderbilt University

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