Hi, We figured out was the problem was. Just so others on the list are aware, when deleting voxels from the brainmask.mgz or brainmask.finalsurfs.manedit.mgz volumes in Freeview, you should verify that the deleted voxels have a value of 1, not 0. The 5.3 version of Freeview has a "Recon Editing" checkbox in the voxel edit window which makes the erasing function (shift + click) set voxels to 1 instead of 0 by default.

Alternatively, you can set the brush value to 1 and just paint in the deleted voxels. You will have to do this if you are using an older version of Freeview. -Louis

On Wed, 28 Aug 2013, Harms, Michael wrote:

If you're following the instructions of the tutorial, then I don't know why your edits to brain.finalsurfs.manedit.mgz wouldn't be reflected in the pial surface. Perhaps one of the FS developers will have a thought as to what is going wrong.

cheers, -MH

--  Michael Harms, Ph.D.

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Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mharms@wustl.edu

From: Francesco Siciliano sicilia@nyspi.columbia.edu Date: Wednesday, August 28, 2013 12:36 PM To: "Harms, Michael" mharms@wustl.edu Subject: RE: [Freesurfer] pial surface editing

My main issue is that the edits I make to brain.finalsurfs.manedit.mgz are not being incorporated into the reconfiguration of the pial surface. What I mean to say is that when I load the pial surface onto the brainmask, the changes that I made to brain.finalsurfs.manedit.mgz, where the pial surface incorrectly extended into the cerebellum, have not been taken into account. The countour of the pial surface that borders that cerebellum has not been altered. Do you have any idea why this may be occurring?

-Francesco

Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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From: Harms, Michael [mharms@wustl.edu] Sent: Wednesday, August 28, 2013 12:19 PM To: Francesco Siciliano; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial surface editing

Are you saying that edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are not showing up as affecting the actual pial surfaces themselves? I would focus on whether the pial surfaces are fixed, not whether edits to brain.finalsurfs.manedit.mgz are "back-propagated" to brainmask.mgz.  (I suspect they are not).

cheers, -MH

--  Michael Harms, Ph.D.

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Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mharms@wustl.edu

From: Francesco Siciliano sicilia@nyspi.columbia.edu Date: Wednesday, August 28, 2013 11:01 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] pial surface editing

Hello,

I am having a few issues with editing the pial surface in freeview. It appears as though the edits I make to the brainmask are not being taken into account when I re-run recon-all. I work on a MacBook Pro and have been using "shift+click" to delete voxels at a brush value of 1 and then saving the brainmask.mgz back into the mri folder. When making edits to the brainmask I have the brainmask highlighted. Upon clicking save, the mri folder contains both brainmask.mgz and brainmask.mgz~ (The version with a ~ seems to indicate the older version of the file based on modification time).

Additionally, the edits that I make to brain.finalsurfs.manedit.mgz for pial surface that has extended into the cerebellum seems to not be taken into account when I re-run recon-all. I have been making a copy of brain.finalsurfs.mgz, pasting it into the mri folder, and renaming it brain.finalsurfs.manedit.mgz. I then load this volume and make edits to it according to the same specifications as the brainmask.mgz. Shouldn't I be able to see changes made to the pial surface in the brainmask.mgz from edits I make to the brain.finalsurfs.manedit.mgz after running recon-all? Neither the brainmask.mgz nor the brain.finalsurfs.mgz take into account the edits I've made on brain.finalsurfs.manedit.mgz. I'm not sure if I'm deleting voxels incorrectly or saving incorrectly. I've tried to troubleshoot several times and keep encountering similar issues.

The version of FreeSurfer that I am working from is: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 My editing interface looks slightly different from the current version explained on the freesurfer wiki. I do not have an option to select recon-editing. Adding control points, however, has been successful. I have been using the command recon-all -autorecon2 -autorecon3 -s subj001

Any help getting to the bottom of this would be greatly appreciated!

Thanks,

Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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