Hi Khadka,
Although it is an old mail (sorry), because this topic came up in
another thread, I reply here also.
You need to edit the brain.finalsurfs.manedit.mgz file. Create this file
by copying :
cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
then edit the manedit file.
Best, Martin
On 01/16/2014 01:07 PM, Khadka, Sankalpa wrote:
Dear freesurfer community,
My question is directed to those who have experience with editing
brain.finalsurfs.mgz.
According to the tutorials, after making edits on
brainmask.finalsurfs.mgz (which is normally done when the pial surface
is not accurate), we can run,
recon-all -autorecon-pial -subjid subj"
However, I found an anomaly when I looked at the steps that
-autorecon-pial flag goes through. The very first step of
autorecon-pial flag is "mri_mask" command. This takes brain.mgz and
brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output.
Now, if we have made edits on brain.finalsurfs.mgz, it will be
overwritten by the new one and hence our edits won't take an effect.
I ran few experiments too.
First, I made edits on brain.finalsurfs.mgz and ran recon-all with
autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my
edits did not make any changes.
Second, I made edits on brain.finalsurfs.mgz and ran with white,
smooth2, inflate2, autorecon3 flag (basically starting from
mri_make_surfaces command). On doing so, the edits made desirable
changes and brain.finalsurfs.mgz remained intact.
Third, I made changes on brainmask.mgz and brain.mgz (inputs for
mri_mask). It also works as expected.
Finally, I also followed the recommended steps from the tutorial by
creating brainmask.finalsurfs.manedit.mgz, however, the edits from
"manedit" were not carried on to brainmask.finalsurfs.mgz
Could anyone please shed some light on this? What would be the best
strategy to follow?
Thank you,
Sankalpa
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--
Martin Reuter, Ph.D.
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
[email protected]
[email protected]
Web : http://reuter.mit.edu
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