---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Tue, Jul 16, 2013 at 12:44 PM Subject: Re: [Freesurfer] subcortical segmentation To: Liane Hunter liane.hunter@med.einstein.yu.edu
Hi Liane
can you cc the list so others can answer? You will get better and faster answers that way, and also others will be able to learn from the replies.
thanks
Bruce
On Tue, 16 Jul 2013, Liane Hunter wrote:
Thanks so much.As as clarification: should I make edits to the
brainmask.mgz
or norm.mgz file. Likewise, is this the correct command to run to fix edits to the subcortical segmentation:
normalization -maskbfs -segmentation -autorecon2-wm -autorecon3.
Thank you again for all of your help Liane
On Tue, Jul 16, 2013 at 11:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Liane the brainmask is not for subcortical segmentation - use the norm.mgz if you want to visualize subcortical structures
cheers Bruce On Tue, 16 Jul 2013, Liane Hunter wrote: Hello, I noticed that when I am checking the subcortical segmentation the brainmask does not accurately display the subcortical structures ( ie. the putamen is too small). The segmentation appears to be correct when I compare it to the original file. Does anyone know why this is the case? Also, if I make changes to the subcortical segmentation based on the original file will this change accurately edit the brainmask? Thank you. Sincerely, LianeLiane HunterMD/Ph.D Candidate Albert Einstein College of Medicine
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