Martin,
Which version of freesurfer did you use to generate the surfaces?
Because the number of topological defects in your surface (64) is very
high. You may have to relaunch the surfaces (orig and pial) to get
better surfaces (i.e. 0 defect).
Lgi often fail if there are defects, sometimes it will pass if you
relaunch it, but if there are numerous defects the algorithm is not
able to cope with it.
Marie
Quoting Martin Kavec <[EMAIL PROTECTED]>:
Hi,
I get the following warning followed by error in LGI calculation:
________________________________________________________
... remeasuring lGI value for vertex iV = 6301. It may take a few minutes.
WARNING -- Problem for vertex iV = 6301, lGI value is aberrantly high
(lGI=48.6447)...
...lGI computation will be stopped. This may be caused by
topological defects,
check mris_euler_number on the pial surface.
ERROR: compute_lgi did not create output
file 'tmp-mris_compute_lgi/rh.pial_lgi.asc'!
Linux antarctica 2.6.24-gentoo-r8 #1 SMP Sat May 17 14:07:35 CEST 2008 x86_64
Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz GenuineIntel GNU/Linux
recon-all exited with ERRORS at Sun May 25 09:22:16 CEST 2008
________________________________________________________
The suggested mris_euler_number gives:
________________________________________________________
mris_euler_number rh.pial
euler # = v-e+f = 2g-2: 155756 - 467454 + 311636 = -62 --> 32 holes
F =2V-4: 311636 != 311512-4 (-128)
2E=3F: 934908 = 934908 (0)
total defect index = 64
________________________________________________________
If I just rerun the LGI calculation, as suggested on the LGI web page, the
calculation stops at exactly the same place. I am not sure, if I understand
the execution correctly in this case, but while observing the commands, one
of the first ones is removing the tmp-.... in the surf directory.
Can anybody suggest me please, how to correct the defect in that particular
vertex. The topological defect repair described on the web deals with dura
matter pixels removal.
Thanks in advance,
Martin
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