1. Is this a contrast-enhanced acquisition? That will make things more difficult, although we have processed them in the past.
2. I think the skull stripping removed some brain tissue, which may be the source of your large defects. Can you please check it and get back to us? This also might be due to the contrast enhancement.
cheers Bruce On Tue, 26 Feb 2013, Blessy M wrote:
I should have send it with an extension. But it is tiff, just as you asked.
On Tue, Feb 26, 2013 at 3:03 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Blessy
what format is this? If you don't send it with an extension there is no
way to know....
Bruce
On Tue, 26 Feb 2013, Blessy M wrote:
Forgot the image. please find attached.
On Tue, Feb 26, 2013 at 2:45 PM, Blessy M <bles...@gmail.com> wrote:
I ran this command, and got the attached image
tkmedit ./ brainmask.mgz lh.inflated.nofix
For some reason tksurfer is not looking good/complete
tksurfer ./ lh inflated
On Tue, Feb 26, 2013 at 11:53 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
you can save a tif of it and post it to the list
On Tue, 26 Feb 2013, Blessy M wrote:
Yes it is still at defect 32.
The tail of the recon-all.log is as follows:
CORRECTING DEFECT 30 (vertices=18, convex hull=22)
After retessellation of defect 30, euler #=-7
(59491,172395,112897) : difference with
theory
(-28) = -21
CORRECTING DEFECT 31 (vertices=244, convex
hull=142)
After retessellation of defect 31, euler #=-6
(59502,172495,112987) : difference with
theory
(-27) = -21
CORRECTING DEFECT 32 (vertices=44865, convex
hull=8969)
Should I attach the lh.inflated.nofix in a
separate email to you, Bruce?
On Tue, Feb 26, 2013 at 10:08 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
is it still on defect 32? What does the
tail of the recon-all.log say? And can
you
send us an image of the
lh.inflated.nofix (if it is the lh that is
running)?
On Tue, 26 Feb 2013, Blessy M wrote:
I verified lh.orig.nofix, and it
looks fine. But, there has been no new
files
created since Saturday
(2/23/2013).
I am considering stopping the process.
I was thinking, I had created a skull
stripped image, and was giving that
as
input to recon-all in the
command below:
recon-all -subjid . -noskullstrip
-autorecon1 -notal-check -autorecon2
-autorecon3
Should -noskullstrip flag be after
autorecon1?
On Mon, Feb 25, 2013 at 3:35 PM, Bruce
Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
try looking at the
lh.inflated.nofix or lh.orig.nofix (or rh,
whichever
one is running) and see if
something is
dramatically wrong (like skull
attached to brain, or hemis
connected,
etc....)
On Mon, 25 Feb 2013, Blessy M
wrote:
Recon is still running. I
started the process on 2/21/2013.
Its been
4 days.
I ran this command, and
viewed the aseg file, and that looks
reasonable
tkmedit ./ brainmask.mgz
-aux T1.mgz -surfs -aseg
Currently it is at this
stage:
Correction of the Topology
Finding true center and
radius of Spherical Surface...done
Surface centered at
(0,0,0) with radius 100.0 in 13 iterations
marking ambiguous
vertices...
124766 ambiguous faces
found in tessellation
segmenting defects...
......
61 defects to be corrected
0 vertices coincident
......
......
CORRECTING DEFECT 31
(vertices=244, convex hull=142)
After retessellation of
defect 31, euler #=-6
(59502,172495,112987)
: difference with theory
(-27) = -21
CORRECTING DEFECT 32
(vertices=44865, convex hull=8969)
On Fri, Feb 22, 2013 at
5:33 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
I don't think
either one of these are errors, just
warnings
that occur pretty
frequently and I
don't think should
impact the results.
Does the recon finish? Do the
results look
ok?
On Fri, 22 Feb
2013, Blessy M wrote:
I am getting
the bottom two sets of errors while
doing a
simple recon-all.
More
specifically while running this command:
recon-all
-subjid . -noskullstrip -autorecon1
-notal-check -autorecon2
-autorecon3
Has someone
encountered this kind of errors? Is
there a
fix?
1)
Computing MAP
estimate using 2772 samples...
********************************************
IFLAG= -1
LINE SEARCH FAILED. SEE DOCUMENTATION
OF
ROUTINE MCSRCH ERROR
RETURN OF
LINE SEARCH: INFO= 6 POSSIBLE CAUSES:
FUNCTION
OR GRADIENT ARE
INCORRECT OR
INCORRECT TOLERANCESoutof
QuasiNewtonEMA:
011: -log(p) =
7296.5 tol
0.000010
...
...
2)
unfolding
failed - restoring original position
--------------------
0146:
dt=13.779160, rms=0.814 (0.000%), neg=0,
invalid=766
blurring
input image with Gaussian with
sigma=0.500...
0000:
dt=0.000, rms=0.814, neg=0, invalid=766
gcamFindOptimalTimeStep: Complete in 101542.133 ms
iter 0,
gcam->neg = 801
......................
unfolding
failed - restoring original position
--------------------
0158:
dt=13.828393, rms=0.814 (-0.069%), neg=0,
invalid=766
blurring
input image with Gaussian with
sigma=0.500...
0000:
dt=0.000, rms=0.814, neg=0, invalid=766
gcamFindOptimalTimeStep: Complete in 100610.148 ms
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