cheers Bruce
p.s. I think this defect is too large - it's about 1/3 of the cortical surface
On Thu, 28 Feb 2013, Blessy M wrote:
The process is still running but nothing new written in the last 24 hrs.
Excerpts from recon-all.log
......
77 defects to be corrected
0 vertices coincident
reading input surface /home/#########/subjects/./surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
.......
CORRECTING DEFECT 20 (vertices=71, convex hull=55)
After retessellation of defect 20, euler #=-3 (58272,166451,108176) :
difference with theory (-54) = -51
CORRECTING DEFECT 21 (vertices=17, convex hull=34)
After retessellation of defect 21, euler #=-2 (58273,166465,108190) :
difference with theory (-53) = -51
CORRECTING DEFECT 22 (vertices=39536, convex hull=7215)
Help!
On Wed, Feb 27, 2013 at 11:37 AM, Blessy M <bles...@gmail.com> wrote:
1. It is not contrast enhanced.
2. I am rerunning recon-all after giving it a manually skull
stripped image. Hopefully this will work.
So basically did this:
recon-all -subjid . -autorecon1 -noskullstrip -notal-check
cp T1.mgz brainmask.auto.mgz
ln -s brainmask.auto.mgz brainmask.mgz
recon-all -subjid . -autorecon2 -autorecon3
On Tue, Feb 26, 2013 at 3:10 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
thanks. I actually meant a tksurfer image, but this
might do. Two questions:
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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