If you have this problem only for one surface, I advise you to recreate the pial surface (recon-all -autorecon2-wm -?h, which will preserve your edits). This will very slightly change the topography of your pial surface. Then you can re-run the recon-all -lgi -?h. In 99.9% of the cases it will solve your problem.

On 19 févr. 10, at 16:16, Lena Palaniyappan wrote:

Hi all

I am running recon-all –localGI
One subjects image is not getting processed and crashes repeatedly with message that there may be a topological defect in a particular vertex. It asks me to check euler number.
The wiki indicates that this crash is a known issue and restrating _mris_compute_lgi must solve this.

My questions are

how to check the euler number and how to interpret this number in terms of topological defects?
mris_compute_lgi does not find lh.pial surface when I TRY TO RESTART - what should I do? I used mris_compute_lgi subjid/surf/lh.pial

Many thanks in advance
Lena
_______________________________________________________
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH

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