Thanks Marie,

Yes at the end I found a threat with the same problem and saw the solution, so I did the recon and re-run the GLI and worked fine, but i didn't re-run the -autorecon3, I would run this separately, I guess it will cause no problems.

Regards,
Gabriel

El 19/10/12, Marie Schaer <Marie.Schaer@unige.ch> escribió:

Hi Gabriel,

It may be the case that because of the surface topology, the lGI fails on one vertex. Most of the time, just recomputing the surface creation solves the problem. Can you try to run recon-all -autorecon2-wm -autorecon3 -randomness -hemi lh -s c_36 and then rerun the lgi computation on this hemisphere?

It should solve the problem. Let me know,

Marie

On Oct 19, 2012, at 3:43 PM, Gabriel Gonzalez Escamilla wrote:

Dear FS experts

I'm trying to calculate the local GI of my subjects but I'm having trouble with one of them, When I run recon-all -s MySubject -localGI it always give me the same message:

... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.
WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)...
...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 '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012

When I checked the mris_euler_number on the pial surface I get no topological defect:

[root@localhost surf]$ mris_euler_number lh.pial
euler # = v-e+f = 2g-2: 134601 - 403797 + 269198 = 2 --> 0 holes
F =2V-4: 269198 = 269202-4 (0)
2E=3F: 807594 = 807594 (0)
total defect index = 0

Also try as: mris_compute_lgi --i lh.pial --echo
And get the following message:

... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.
WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)...
...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.
endif
endif
echo ""
echo
rm -f ${MLF}
rm -f /tmp/clgi_15928_.m
if ( $RunIt && ! -e ${tmpdir}/${input}_lgi.asc ) then
if ( 1 && ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) then
echo "ERROR: compute_lgi did not create output file '${tmpdir}/${input}_lgi.asc'!"
echo ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
exit 1
exit 1

The right hemisphere works perfectly...with this last command, but left just does not work.
Any ideas about this? any way to fix it??? Can anyone help me?

Best Regards,
Gabriel

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