Hello,
I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages:
³... remeasuring lGI value for vertex iV = 65101. It may take a few minutes. WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high (lGI=56.5472)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.²
³mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 143555 - 430659 + 287106 = 2 --> 0 holes F =2V-4: 287106 = 287110-4 (0) 2E=3F: 861318 = 861318 (0)
total defect index = 0²
³mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 65560 - 196674 + 131116 = 2 --> 0 holes F =2V-4: 131116 = 131120-4 (0) 2E=3F: 393348 = 393348 (0)
total defect index = 0²
I re-run the recon-all -s 01_097_Y0 -hemi lh -autorecon2 autorecon3 and recon-all -s 01_097_Y0 -localGI
It stopped at the same vertex.
Could you please let me know anything I can do to overcome this issue? Thank you very much.
Wayne
Wayne,
You can try to rerun the surface reconstruction (recon-all -autorecon2-wm -randomness, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know.
Marie
On Jun 27, 2011, at 10:32 PM, Wayne Su wrote:
Hello,
I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages:
“... remeasuring lGI value for vertex iV = 65101. It may take a few minutes. WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high (lGI=56.5472)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.”
“mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 143555 - 430659 + 287106 = 2 --> 0 holes F =2V-4: 287106 = 287110-4 (0) 2E=3F: 861318 = 861318 (0)
total defect index = 0”
“mris_euler_number ./lh.pial-outer-smoothed
euler # = v-e+f = 2g-2: 65560 - 196674 + 131116 = 2 --> 0 holes F =2V-4: 131116 = 131120-4 (0) 2E=3F: 393348 = 393348 (0)
total defect index = 0”
I re-run the recon-all -s 01_097_Y0 -hemi lh -autorecon2 –autorecon3 and recon-all -s 01_097_Y0 -localGI
It stopped at the same vertex.
Could you please let me know anything I can do to overcome this issue? Thank you very much.
Wayne _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Marie:
I have the same problem. I am doing LGI on a group of Genetic High Risk (for Schizophrenia) subjects (n=77).
Here is what I got for one brain: * WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high (lGI=47.4609)... ...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 '/usr/local/freesurfer/subjects/HM5103/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! Linux NeuroImage-Gamma 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Tue Jun 28 06:20:34 EDT 2011*
Do I do the same thing that you recommended?
thanks,
Alan
On Tue, Jun 28, 2011 at 4:53 AM, Marie Schaer Marie.Schaer@unige.ch wrote:
Wayne,
You can try to rerun the surface reconstruction (recon-all -autorecon2-wm *-randomness*, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know.
Marie
On Jun 27, 2011, at 10:32 PM, Wayne Su wrote:
Hello,
I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages:
“... remeasuring lGI value for vertex iV = 65101. It may take a few minutes. WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high (lGI=56.5472)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.”
“mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 143555 - 430659 + 287106 = 2 --> 0 holes F =2V-4: 287106 = 287110-4 (0) 2E=3F: 861318 = 861318 (0)
total defect index = 0”
“mris_euler_number ./lh.pial-outer-smoothed
euler # = v-e+f = 2g-2: 65560 - 196674 + 131116 = 2 --> 0 holes F =2V-4: 131116 = 131120-4 (0) 2E=3F: 393348 = 393348 (0)
total defect index = 0”
I re-run the recon-all -s 01_097_Y0 -hemi lh -autorecon2 –autorecon3 and recon-all -s 01_097_Y0 -localGI
It stopped at the same vertex.
Could you please let me know anything I can do to overcome this issue? Thank you very much.
Wayne _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Alan,
If you only have this problem with one or just a few subjects, then I am pretty confident that running recon-all -autorecon2-wm -randomness will solve your problem. Otherwise let me know!
Marie
On Jun 28, 2011, at 3:48 PM, Alan Francis wrote:
Hi Marie:
I have the same problem. I am doing LGI on a group of Genetic High Risk (for Schizophrenia) subjects (n=77).
Here is what I got for one brain:
WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high (lGI=47.4609)... ...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 '/usr/local/freesurfer/subjects/HM5103/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! Linux NeuroImage-Gamma 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Tue Jun 28 06:20:34 EDT 2011
Do I do the same thing that you recommended?
thanks,
Alan
On Tue, Jun 28, 2011 at 4:53 AM, Marie Schaer Marie.Schaer@unige.ch wrote:
Wayne,
You can try to rerun the surface reconstruction (recon-all -autorecon2-wm -randomness, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know.
Marie
On Jun 27, 2011, at 10:32 PM, Wayne Su wrote:
Hello,
I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages:
“... remeasuring lGI value for vertex iV = 65101. It may take a few minutes. WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high (lGI=56.5472)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.”
“mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 143555 - 430659 + 287106 = 2 --> 0 holes F =2V-4: 287106 = 287110-4 (0) 2E=3F: 861318 = 861318 (0)
total defect index = 0”
“mris_euler_number ./lh.pial-outer-smoothed
euler # = v-e+f = 2g-2: 65560 - 196674 + 131116 = 2 --> 0 holes F =2V-4: 131116 = 131120-4 (0) 2E=3F: 393348 = 393348 (0)
total defect index = 0”
I re-run the recon-all -s 01_097_Y0 -hemi lh -autorecon2 –autorecon3 and recon-all -s 01_097_Y0 -localGI
It stopped at the same vertex.
Could you please let me know anything I can do to overcome this issue? Thank you very much.
Wayne _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Alan Francis -
Marie Schaer -
Wayne Su