On Tue, Feb 26, 2013 at 3:03 PM, Bruce Fischl
<fischl@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 <blessam@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 <fischl@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 <fischl@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 <fischl@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
<fischl@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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