Dear Octavian,
the current philosophy with wm.mgz edits is not to directly affect voxel values
in original T1 image.
The wm.mgz serves as starting point for the white surface estimation. The
?h.white surface is estimated according gradient in voxel values in
brain.finalsurfs.mgz (which is, basically, preprocessed T1 image) using
basically preprocessed surfaces obtained from wm.mgz (?h.orig) as a starting
position where to search for intensity gradient.
The editing of wm.mgz helps to find out the GM/WM itensity gradient and
properly place ?h.white there.
Therefore, where there is insufficient GM/WM contrast, the wm.mgz cannot help
out. I think that there is no change in the behavior between v5.3 and v6.0 in
this aspect. I have seen many cases where wm.mgz edit does not help to improve
?h.white surfaces in the data processed by v5.3.
There is an -overlay option in mris_make_surfaces which explicitly modifies
voxel values in input image for mris_make_surfaces (brain.finalsurfs.mgz as
default in recon-all). However, this option only works for cases when wm.mgz is
extended, not deleted:
In voxels which have value 255 in wm.mgz, it replaces current voxel value in
input image by desired value of white matter. This option is currently not used
in recon-all.
I would opt for implementation of similar option for deletion of voxels in
wm.mgz: Where wm.mgz voxel values equal 1, to replace input image voxel values
by desired values of GRAY matter. This should force ?h.white to directly follow
edits of wm.mgz
As for editing of 001.mgz, beware the pitfall with editing images with mutually
different geometry in FreeView I posted today:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52729.html
Antonin Skoch
Dear All,
Regarding wm.mgz edits not incorporated into wm surface, which seems to
have been reported on by several of us with FS 6.00. I followed Antonin's
idea of editing 001.mgz by switching wm-intensity voxels clearly not wm
(mostly in the subtemporal regions, at times close to bright dural portions
in the crown) to gm intensities and ran recon-all -all, and this time all
was OK. So it seems that the problem is that on re-initializing during
-autorecon2-wm rerun, the routine does not edit out high intensity voxels
even if manually excluded in wm.mgz. This seems to be different to some
extent with how FS 5.3 was reacting, although I did not look at this
systematically. There may be a reason that manual editing is just part of
the story during rerun and does not automatically override the recon
stream, but I do not know it.
Octavian
---------- Forwarded message ----------
From: Octavian Lie <octavian....@gmail.com>
Date: Sun, Apr 2, 2017 at 7:59 PM
Subject: wm edits not incorporated
To: octavian lie <octavian....@gmail.com>
Dear Bruce,
I just transferred subject r02.tar.gz.
Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
on reruns using any of the
recon-all -autorecon-wm -aitorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all
FOr example, the complete command line for a rerun is
recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
-parallel > output.txt &
Here are some of the edited voxels which are not excluded from the wm on
rerun:
-40.14, -2.67, 116.29 coronal slice 132
12.73, -23.67, 126.16 coronal slice 171
14.05, 12.33, 11.61 coronal slice 147
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