Hi Doug,
so you
1. edited the cross sectionals and surfaces look fine (make sure you
edit the brain.finalsurfs.manedit.mgz file, which you create as a
copy of the brain.finalsurfs.mgz)
2. checked/edited the base and surfaces look fine too
3. ran the longitudinal from scratch (w/o any edits)
and then in the long, the surface looks not good?
Edits should automatically be copied from cross->long (if the
manedit file exist). Surfaces are taken from the base to initialize
longitudinal processing. That is why both step1 and step2 above are
important. Step3 is a good idea to make sure that the longs are not
polluted by some earlier edits. For example edits from cross are
only copied over if the long has no manedit file, else only the
edits in the long will be used. (I think this also answers some of
the questions in the archive mail 1 you cite below, the archive mail
2 is a question about cross sectional processing, but I think there
the problem is that brainmask.finalsurfs.mgz was edited directly,
not the manedit file, so edits probably get overwritten).
I also have the feeling that we fixed something about the editing in
longitudinal processing after 5.1, but cannot find it documented on
the wiki (so not sure). You may want to try to run this with 5.3 if
it does not work with 5.1
Best, Martin
On 05/02/2014 10:45 AM, Douglas
Merkitch wrote:
Dear Freesurfer
experts,
I have a question
regarding longitudinal edits. Specifically the
brain.finalsurfs.manedit.mgz file and the longitudinal
processing stream in Freesufer 5.1 on a Mac
(freesurfer-i686-apple-darwin9.8.0-stable5-20110525).
The problem that I am
having is that the edits saved in the
brain.finalsurfs.manedit.mgz file do not carry over when
processing longitudinally.
Previous posts have
addressed this topic, but have not (to my knowledge) solved the
issue. Please see the threads from the Freesurfer archive below
for a brief context:
Please let me know if
more information is needed to understand the issue.
Any insight/ideas
regarding this issue would be greatly appreciated!
Thanks,
Doug
Doug Merkitch
Neurological
Sciences
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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:
mreuter@nmr.mgh.harvard.edu
reuter@mit.edu
Web : http://reuter.mit.edu