this is a known bug. We'll have a fix soon. You can change the mri_fill
call in recon-all to use aseg.auto.mgz as a quick fix.
On Fri,
14 Dec 2007, Michael Harms wrote:
Hello,
Just a brief addendum:
Our previous experience with -autorecon2 has been primarily with v3.0.5
(and thus v3.0.5 asegs, not 4.0.1 asegs as Matt initially indicated)
where we have never encountered this "nbrs" error during mri_fill. We
have just started processing some new brains through -autorecon2 using
v4.0.1, and 2 of 12 brains so far have already had this error. We are
wondering if the problem might be because voxels now labelled as
callosum under v4.0.1 are not considered as candidates for identifying
lh and rh wm neighbors...?
- Mike H.
On Fri, 2007-12-14 at 15:08 -0600, Matt Colvin wrote:
Dear FreeSurfer folks,
We recently had an error occur while processing two brains in recon2. We
are using FreeSurfer version 4.0.1 for these subjects. The error message
in both cases mentions that mri_fill could not find points where lh and rh
wm were "nbrs" (I assume this is short for neighbors).
Upon inspecting the aseg.mgz files for both brains, I found that, while
there were one or two spots in each brain where lh and rh wm voxels did
touch, it was much less than in other version 4.0.1 asegs that we have
processed and inspected. In other words, there were plenty of places where
the connection between the l and r wm was mediated by the corpus callosum
label, but almost none where the wm were direct neighbors.
Is there any way known for fixing this problem? Could it be related to the
new corpus callosum label in the version 4 segmentation which was not
present in earlier versions?
Thanks in advance for any help anybody might be able to lend.
Here is the end of the error message:
#--------------------------------------------
[EMAIL PROTECTED] Fill Fri Dec 14 07:12:09 CST 2007
/disk/conte_raid1/freesurfer/Geller/02681/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
1.033 -0.026 0.146 -14.846;
0.010 1.114 0.190 -60.985;
-0.140 -0.203 0.988 38.624;
0.000 0.000 0.000 1.000;
voxel to talairach voxel transform
1.033 -0.026 0.146 -14.846;
0.010 1.114 0.190 -60.985;
-0.140 -0.203 0.988 38.624;
0.000 0.000 0.000 1.000;
reading segmented volume aseg.mgz...
mri_fill: could not find any points where lh and rh wm are nbrs
Linux eureka 2.6.9-22.0.2.ELsmp #1 SMP Thu Jan 5 17:13:01 EST 2006 i686
i686 i386 GNU/Linux
recon-all exited with ERRORS at Fri Dec 14 07:12:31 CST 2007
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