Hello,
After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz, and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of some subcortical structures (specifically the hippocampus, amygdala, and accumbens) had changed, even though I did not edit aseg.mgz. Is that to be expected?
Most of the differences were minimal, a 5% change or less. However some of the structures changed by as much as 10 or 15%. I am preparing to do a second-level analysis of ROIs of the hippocampus and amygdala on a group of subjects. Given that cortical edits seem to influence subcortical structure volumes, would it be unreliable to run a second-level analysis with subcortical volumes recorded prior to cortical editing?
Thank you,
-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
what version are you running? On Mon, 7 Oct 2013, Francesco Siciliano wrote:
Hello, After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz, and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of some subcortical structures (specifically the hippocampus, amygdala, and accumbens) had changed, even though I did not edit aseg.mgz. Is that to be expected?
Most of the differences were minimal, a 5% change or less. However some of the structures changed by as much as 10 or 15%. I am preparing to do a second-level analysis of ROIs of the hippocampus and amygdala on a group of subjects. Given that cortical edits seem to influence subcortical structure volumes, would it be unreliable to run a second-level analysis with subcortical volumes recorded prior to cortical editing?
Thank you,
-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
My freesurfer version document reads as follows: freesurfer-i686-apple-darwin9.8.0-stable5-20110525
I am running freeview 5.3 ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 3:51 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] changes to subcortical volumes
what version are you running? On Mon, 7 Oct 2013, Francesco Siciliano wrote:
Hello, After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz, and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of some subcortical structures (specifically the hippocampus, amygdala, and accumbens) had changed, even though I did not edit aseg.mgz. Is that to be expected?
Most of the differences were minimal, a 5% change or less. However some of the structures changed by as much as 10 or 15%. I am preparing to do a second-level analysis of ROIs of the hippocampus and amygdala on a group of subjects. Given that cortical edits seem to influence subcortical structure volumes, would it be unreliable to run a second-level analysis with subcortical volumes recorded prior to cortical editing?
Thank you,
-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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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Francesco Siciliano