can you cc the list? So all you did was change some voxels from hippocampus to amygdala?
On Tue, 28 Jan 2014, Thomas Fink wrote:
Hi Bruce,
Sorry, these were .tifs. Now they are...
Thanks
On Mon, Jan 27, 2014 at 11:48 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
Hi Thomas
what format are these in? Can you include extensions in the
files you send in the future?
thanks
Bruce
On Mon, 27 Jan 2014, Thomas Fink wrote:
Hi Bruce,
At the moment we are interested in the volumes and
thus we checked and
corrected the aseg-file (corrections done as
described in the
RecommendedReconstructions).
In the first attachment you can see the incorrect
automatic segementation of
the hippocampus and in the second what it looked
like after our corrections,
but before the new recon with the giant defect.
Cheerio,
Thomas
On Thu, Jan 23, 2014 at 10:39 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Thomas
when you say errors in the hippocampus do you
mean the aseg or
the surfaces? If the surfaces, don't worry
about them as they
are not used in the hippocampal region. You
are probably
connecting the temporal lobe to the main body
of the white
matter creating a giant defect.
cheers
Bruce
On Mon, 20 Jan 2014, Thomas Fink wrote:
Dear Freesurfer experts,
We are using FS 5.1 and have several
participants
with errors in the
segmentation of the hippocampus and
other regions of
the cortex. So far we
did corrections to the hippocampus but
in 10 out of
13 participants we got
error messages listed below:
Seven participants:
-----
CORRECTING DEFECT 0 (vertices=74686,
convex
hull=1605)
Excessive topologic defect encountered:
could not
allocate 390335770 edges
for retessellation
Cannot allocate memory
Darwin NPSY.local 12.4.0 Darwin Kernel
Version
12.4.0: Wed May 1 17:57:12
PDT 2013;
root:xnu-2050.24.15~1/RELEASE_X86_64
x86_64
-----
One participant:
-----
mhtVoxelList_Add(189, 240, 290, 260205):
complete
list too big!
mhtVoxelList_Add(189, 240, 290, 260205):
complete
list too big!
No such file or directory
marking ambiguous vertices...
Too many intersected faces for face
255461 (126442,
128896, 128873)
No such file or directory
Darwin NPSY.local 12.4.0 Darwin Kernel
Version
12.4.0: Wed May 1 17:57:12
PDT 2013;
root:xnu-2050.24.15~1/RELEASE_X86_64
x86_64
-----
One participant:
-----
CORRECTING DEFECT 14 (vertices=33317,
convex
hull=1285)
mris_fix_topology(26738) malloc: ***
mmap(size=1212047360) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in
malloc_error_break to debug
Bus error
Darwin NPSY.local 12.4.0 Darwin Kernel
Version
12.4.0: Wed May 1 17:57:12
PDT 2013;
root:xnu-2050.24.15~1/RELEASE_X86_64
x86_64
-----
One participant:
-----
Correction of the Topology
Finding true center and radius of
Spherical
Surface...done
Surface centered at (0,0,0) with radius
100.0 in 11
iterations
marking ambiguous vertices...
414500 ambiguous faces found in
tessellation
segmenting defects...
Bus error
Darwin NPSY.local 12.4.0 Darwin Kernel
Version
12.4.0: Wed May 1 17:57:12
PDT 2013;
root:xnu-2050.24.15~1/RELEASE_X86_64
x86_64
-----
The error log says in all cases that
there is
something wrong with the
cerebellum. When we open the ?h
inflated.nofix file
then we see the
cerebellum added (see attached file) in
the
hemisphere we made the edits.
We have no clue if or what we are doing
wrong and
here are the steps we
did:
- open the files (tkmedit subject
norm.mgz
-aseg.mgz
- Tool -> Configure Segmentation Brush
info ->
select the hippocampus -> add
voxels
- File -> save segmentation
- run recon with "recon-all -autorecon2
-noaseg
–autorecon3 -subjid subject
-nuintensitycor-3T"
So far we had no problems with our
subjects for all
the previous steps
(recon after wm, pial, .... edits) and
it did run
smoothly.
Any help would be greatly appreciated.
Thomas Fink Mail: Thomas.Fink@psy.lmu.de
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