On Tue, 28 Jan 2014, Thomas Fink wrote:
Yes, all we did in this case was change amygdala to hippocampus and in other
cases white matter to hippocampus or vice versa.
Thomas Fink Doktorand & wiss. Mitarb.
Lehrstuhl für Neuropsychologie Mail: thomas.f...@psy.lmu.de
Phone: +49(0)89/2180-3123
On Tue, Jan 28, 2014 at 2:32 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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
<fis...@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
<fis...@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.f...@psy.lmu.de
The information in this e-mail is
intended only for
the person to whom
it is
addressed. If you believe this e-mail
was sent to
you in error and the
e-mail
contains patient information, please
contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline .
If the
e-mail was sent to you
in error
but does not contain patient
information, please
contact the sender
and properly
dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
