Dear Christian,
I am aware that the lGI may occasionnally exit with the error you
mentionned in some rare cases of pial surfaces with normal euler
neumbers. I am working on debugging it.
In the mean time, if this is only for one subject, is it possible for
you to recreate the surfaces just for the hemisphere where you have
this problem (i.e. relaunching recon-all -hemi ?h -autorecon2 and
-autorecon3)? This would probably be the easiest way to overcome the
aberrantly high lGI issue, as it will change very slightly the
position and the total number of vertices of the white and pial
surfaces, which will normally solve the problem. However, that implies
that you would have to redo any statistical analyses that you may have
already done on cortical thickness or cortical volumes (but there is
no reason that the results would change just with reprocessing one
hemisphere with the same freesurfer version).
Let me know how it goes,
Marie
Quoting Christian Scheel <[email protected]>:
Dear all,
I have successfully run 'recon-all -lgi' for all my subjects. However
the computation process stopped in one of the brains claiming an lGI
vertex value was aberrantly too high and giving me the following error
message:
#####
... remeasuring lGI value for vertex iV = 32501. It may take a few minutes.
WARNING -- Problem for vertex iV = 32501, lGI value is aberrantly high
(lGI=40.5282)...
...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
'/home/freesurfer/christian/34/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'!
#####
I have already restarted the computation twice without success. The
script always crashes at the same vertex. The error message and the
wiki page mention such an error in connection with possible topological
defects. However when I check the mris_euler_number for the subject's
rh.pial it interestingly does not show me any topological defect. Here
is the output:
#####
[freesur...@localhost ~/christian]$ mris_euler_number
/home/freesurfer/christian/34/surf/rh.pial
euler # = v-e+f = 2g-2: 133775 - 401319 + 267546 = 2 --> 0 holes
F =2V-4: 267546 = 267550-4 (0)
2E=3F: 802638 = 802638 (0)
total defect index = 0
#####
In all other brains the lGI calculation was successful. Does anyone of
you have an idea? Any help is greatly appreciated.
Best wishes,
Christian Scheel
---
University of Cologne
Department of Psychiatry
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