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:
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... 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'!
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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:
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[freesurfer@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
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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