Re: [Freesurfer] The results of your email commands
Hello, The files didnt work! Here is the error after trying 2 participants, one with each mri_segstats you attached. same error for both. Could you please let me know what to do next? n#- #@# Curvature Stats rh Tue May 24 08:13:18 JST 2016 /Users/dave/Documents/tot/Studies/ASD_Struct/Kj/Surf_test/PSY1012fs/surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PSY1012fs rh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface[ PSY1012fs/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [] [ ok ] Determining KH curvatures... [] [ ok ] Determining k1k2 curvatures... [] [ ok ] deltaViolations [ 260 ] Gb_filter = 0 WARN:S lookup min: -0.175830 WARN:S explicit min: 0.00vertex = 422 # #@# ASeg Stats Tue May 24 08:13:23 JST 2016 \nINFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /Users/dave/Documents/tot/Studies/ASD_Struct/kj/Surf_test/PSY1012fs \n mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/freesurfer/ASegStatsLUT.txt --subject PSY1012fs \n $Id: mri_segstats.c,v 1.110.2.3 2015/07/02 20:12:19 zkaufman Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/freesurfer/ASegStatsLUT.txt --subject PSY1012fs sysname Darwin hostname daves-Mac-Pro.local machine x86_64 user dave UseRobust 0 atlas_icv (eTIV) = 1512862 mm^3(det: 1.287696 ) Computing euler number orig.nofix lheno = -122, rheno = -128 orig.nofix lhholes = 62, rhholes = 65 Loading mri/aseg.mgz Warning: cannot find /Users/dave/Documents/tot/Studies/ASD_Struct/kj/Surf_test/PSY1012fs/mri/ribbon.mgz, not computing whole brain stats Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #-- Started at Mon May 23 11:43:42 JST 2016 Ended at Tue May 24 08:16:38 JST 2016 #@#%# recon-all-run-time-hours 20.549 recon-all -s PSY1012fs finished without error at Tue May 24 08:16:38 JST 2016 done [daves-Mac-Pro:ASD_Struct/kj/Surf_test] dave% From: davema...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 20 May 2016 01:07:28 + Subject: Re: [Freesurfer] The results of your email commands Thanks a lot. Does the snowleaopard version work on El Capitan? So by replacing the version already found in bin/mrisegstats, with the leopard one after Chomd +x, it should work? I thought i would get a link for something like mri_segstats.ElCapitan? Yas > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Thu, 19 May 2016 11:07:40 -0400 > Subject: Re: [Freesurfer] The results of your email commands > > I've refreshed those links > > On 05/18/2016 10:44 PM, Dave Yas wrote: > > Dear Doug, > > > > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of > > -autorecon2. > > I saw your answer for others about this Q before and i know how to > > solve this *IF* i was able to access to the links you posted. > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6 > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard > > > > I thought that these should g
Re: [Freesurfer] The results of your email commands
Thanks a lot. Does the snowleaopard version work on El Capitan? So by replacing the version already found in bin/mrisegstats, with the leopard one after Chomd +x, it should work? I thought i would get a link for something like mri_segstats.ElCapitan? Yas > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Thu, 19 May 2016 11:07:40 -0400 > Subject: Re: [Freesurfer] The results of your email commands > > I've refreshed those links > > On 05/18/2016 10:44 PM, Dave Yas wrote: > > Dear Doug, > > > > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of > > -autorecon2. > > I saw your answer for others about this Q before and i know how to > > solve this *IF* i was able to access to the links you posted. > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6 > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard > > > > I thought that these should give me some kind of a pop up to prompt me > > to enter as a guest and get the file to put it in bin/mrisegstats > > But its not doesin anything. > > Also im running OSX El capitan. > > Is there any link that i can visit to download the missing mrisegstats > > file? > > > > Thanks, > > > > Yas > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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.
Re: [Freesurfer] The results of your email commands
I've refreshed those links On 05/18/2016 10:44 PM, Dave Yas wrote: > Dear Doug, > > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of > -autorecon2. > I saw your answer for others about this Q before and i know how to > solve this *IF* i was able to access to the links you posted. > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6 > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard > > I thought that these should give me some kind of a pop up to prompt me > to enter as a guest and get the file to put it in bin/mrisegstats > But its not doesin anything. > Also im running OSX El capitan. > Is there any link that i can visit to download the missing mrisegstats > file? > > Thanks, > > Yas > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
