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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