Hi P,
usually edits to surfaces should not be required in the long. The
surfaces there get initialized from the base, so you need to make sure
the base surface is as accurate as possible. Several edits also get
transferred automatically from the cross sectional runs. See this
http://freesurfer.net/fswiki/LongitudinalEdits
for a description of the different edits, and where they should be done.
About where to restart after making the edits, everything should be done
the same way as in the regular (cross sectional) processing.
So you specifically ask about:
- brainmask edits
- brainfinalsurf edits
- and manual aseg edits.
I just looked at the description of those regular edits
http://freesurfer.net/fswiki/Edits
but sadly there it does not say where to start re-run either. I'll try
to find out and update that soon.
I hope someone with editing experience can chime in and tell us. (I
changed the subject, so that it get's read).
Cheers, Martin
On 04/20/2015 09:44 AM, Bruce Fischl wrote:
I'll leave the first question for Martin but it looks right to me
(except for the typo in what should be "-autorecon3"). For the second
one I think you want to rerun the mri_segstats and
mris_anatomical_stats commands, which should be done by autorecon3
cheers
Bruce
On Mon, 20 Apr 2015, prasser wrote:
Dear All,
I wanted to check that corrections to a Long pial surface through edits
to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the
command:
recon-all -long tpN1 templateID -autorecon2-pial -autorecom3
Is this correct?
Also, after editing the Long aseg.mgz to correct the volume of
structures
what command should be run to have these edits update the dependent
files?
Thanks,
P
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Dr. Martin Reuter
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
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reu...@mit.edu
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