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.lie@gmail.com>
Date: Sun, Apr 2, 2017 at 7:59 PM
Subject: wm edits not incorporated
To: octavian lie <octavian.lie@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

I mention this is not the only subject where I have this problem.

Thank you for your help.

Octavian