Hi Folks
I am using Freesurfer 5.1 and I get the following error: "ERROR:
_FindFacePath: could not find path!"
Is this is a memory related issue ? The same case went through smoothly
with
Freesurfer 5.0.
Also I have not seen this error over a large number of subjects and I
thought it might be system related,
but even when I re-run it, I get the same error.
From the recon-all.error file, the last command is "mris_topo_fixer -mgz
-warnings -seed 1234 ms0709_01 rh"
Here is a small snippet from the recon-all.log file (just before the
error)
Correcting Topology of defect 28 with euler number -1 (1 loops)
computing statistics for defect 28: 288 vertices
location: [ (106,175,134) - average intensity = 89.717 ]
-gray ( 85.29 , 6.61 ) -white ( 95.96 , 3.49 )
-gray ( 83.95 , 18.89 ) -white ( 98.95 , 17.00 )
-intensity (85.286896 [log = -2.118856 ]- 95.961853 [log = -2.118159
] )
-curv (k1=-0.131 (0.556) , r1 = 7.623 | k2=-0.051 (0.131), r2 =
19.605
)
-curv (k1=-0.105 (0.609) , r1 = 9.520 | k2=-0.023 (0.212), r2 =
42.735
)
max face = 548(548) - loop = 1 (1) - ntries = [83,229]
BEST FITNESS (o)is -6.78736
mri =0.000 curv = 1.594 unmri = 0.410
( f=0.00 , v=0.00 , c=1.59 , q= 3.19 )
( f=0.00 , v=0.00 , c=1.59 , q= 3.19 )
BEST FITNESS (M) is -6.40381
mri =0.000 curv = 2.115 unmri = -2.054
( f=0.00 , v=0.00 , c=2.11 , q= 4.23 )
( f=0.00 , v=0.00 , c=2.11 , q= 4.23 )
ERROR: _FindFacePath: could not find path!
Thanks
Mehul
On Wed, Oct 26, 2011 at 6:03 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi
you probably ran out of memory. That's a giant defect so
something is
badly wrong. Check to make sure that the hemis are separated and
that the
skull and cerebellum aren't attached
Bruce
On Wed, 26 Oct 2011, Sindhuja Tirumalai
Govindarajan wrote:
> Hi all,
>
> I got the following error while running recon-all on a patient
dataset.
> Kindly let me know how to proceed.
>
> Thanks!
> Sindhuja
>
>
> 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...
> 129422 ambiguous faces found in tessellation
> segmenting defects...
> 51 defects found, arbitrating ambiguous regions...
> analyzing neighboring defects...
> -merging segment 1 into 0
> -merging segment 2 into 0
> -merging segment 8 into 0
> -merging segment 5 into 7
> -merging segment 28 into 12
> -merging segment 35 into 31
> -merging segment 47 into 43
> 44 defects to be corrected
> 0 vertices coincident
> reading input surface
> /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/
lh.qsphere.nofix...
> reading brain volume from brain...
> reading wm segmentation from wm...
> Computing Initial Surface Statistics
> -face loglikelihood: -9.5482 (-4.7741)
> -vertex loglikelihood: -6.9824 (-3.4912)
> -normal dot loglikelihood: -3.5307 (-3.5307)
> -quad curv loglikelihood: -5.9945 (-2.9973)
> Total Loglikelihood : -26.0558
>
> CORRECTING DEFECT 0 (vertices=50712, convex hull=8198)
> Segmentation fault
>
> recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31
EDT 2011
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
_______________________________________________
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.
