[Freesurfer] local GI calculation Error
Dear FS expertsI'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/Linuxrecon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012When I checked the mris_euler_number on the pial surface I get no topological defect:[root@localhost surf]$ mris_euler_number lh.pialeuler # = 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 = 0Also try as: mris_compute_lgi --i lh.pial --echoAnd 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.endifendifecho echorm -f ${MLF}rm -f /tmp/clgi_15928_.mif ( $RunIt ! -e ${tmpdir}/${input}_lgi.asc ) thenif ( 1 ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) thenecho 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 1exit 1The 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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Re: [Freesurfer] local GI calculation Error
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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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.
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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
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Re: [Freesurfer] local GI calculation Error
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,GabrielEl 19/10/12, Marie Schaer marie.sch...@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 expertsI'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/Linuxrecon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012When I checked the mris_euler_number on the pial surface I get no topological defect:[root@localhost surf]$ mris_euler_number lh.pialeuler # = 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 = 0Also try as: mris_compute_lgi --i lh.pial --echoAnd 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.endifendifecho echorm -f ${MLF}rm -f /tmp/clgi_15928_.mif ( $RunIt ! -e ${tmpdir}/${input}_lgi.asc ) thenif ( 1 ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) thenecho 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 1exit 1The 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
___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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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
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