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
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.
