|
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.
-----------------------------------------------------------
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: mha...@wustl.edu
From: Francesco Siciliano <sici...@nyspi.columbia.edu>
Date: Wednesday, August 28, 2013 12:36 PM To: "Harms, Michael" <mha...@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
From: Harms, Michael [mha...@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.
-----------------------------------------------------------
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: mha...@wustl.edu
From: Francesco Siciliano <sici...@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
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.
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. |
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
