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 1. how to check the euler number and how to interpret this number in terms of topological defects? 2. 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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Dear Lena,
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.
Let me know if it doesn't work,
Marie
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
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
i think you may want to add the flag -randomness to the end of the recon-all command, if your intention is to rerun the topo fixer with different initial conditions (a different seed to the RNG). beginning with v4.5, the default was made to run with -norandomness to preserve the same surface from run to run (which doesnt help in this case).
n.
On Sat, 2010-02-20 at 14:24 +0100, Marie Schaer wrote:
Dear Lena,
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.
Let me know if it doesn't work,
Marie
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 1. how to check the euler number and how to interpret this number in terms of topological defects? 2. 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
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Nick Schmansky