Bruce found that the data had the direction cosine wrong. I have fixed the direction and I'm running it again.
I've put the data in the ftp --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Tue, Dec 18, 2012 at 8:41 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu>wrote: > PPJ, > > Hi, if you want, you can send me the input files (the two aseg's and the > lta) and i can try to replicate the segfault in a debugger. > > also, if you want, there is a beta of the upcoming v5.2 which is posted > here: > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ > which you could try. hopefully that mri_cc doesnt segfault. > > Nick > > > > On Tue, 2012-12-18 at 12:46 -0200, Pedro Paulo de Magalhães Oliveira > Junior wrote: > > I'm having a segfault with mri_cc it's happening sometimes using > > FreeSurfer 5.1 > > > > > > Searching the mailing list I saw a similar problem in 2008 but with no > > answers. > > > > > > The relevant portion of recon-all.log: > > > > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz > > -lta > /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta > c70eb728-c505-46c2-a2a1-1ed409c36ea1 > > > > > > will read input aseg from aseg.auto_noCCseg.mgz > > writing aseg with cc labels to aseg.auto.mgz > > will write lta > > as > /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta > > reading aseg > > from > /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz > > reading norm > > from > /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz > > 2358 voxels in left wm, 13846 in right wm, xrange [122, 136] > > searching rotation angles z=[-10 4], y=[-31 -17] > > ^Msearching scale 1 Z rot -9.8 ^Msearching scale 1 Z rot -9.5 > > ^Msearching scale 1 Z rot -9.3 ^Msearching scale 1 Z rot -9.0 > > ^Msearching scale 1 Z rot -8.8 ^Msearching scale 1 Z rot -8.5 > > ^Msearching scale 1 Z rot -8.3 ^Msearching scale 1 Z rot -8.0 > > ^Msearching scale 1 Z rot -7.8 ^Msearching scale 1 Z rot -7.5 > > ^Msearching scale 1 Z rot -7.3 ^Msearching scale 1 Z rot -7.0 > > ^Msearching scale 1 Z rot -6.8 ^Msearching scale 1 Z rot -6.5 > > ^Msearching scale 1 Z rot -6.3 ^Msearching scale 1 Z rot -6.0 > > ^Msearching scale 1 Z rot -5.8 ^Msearching scale 1 Z rot -5.5 > > ^Msearching scale 1 Z rot -5.3 ^Msearching scale 1 Z rot -5.0 > > ^Msearching scale 1 Z rot -4.8 ^Msearching scale 1 Z rot -4.5 > > ^Msearching scale 1 Z rot -4.3 ^Msearching scale 1 Z rot -4.0 > > ^Msearching scale 1 Z rot -3.8 ^Msearching scale 1 Z rot -3.5 > > ^Msearching scale 1 Z rot -3.3 ^Msearching scale 1 Z rot -3.0 > > ^Msearching scale 1 Z rot -2.8 ^Msearching scale 1 Z rot -2.5 > > ^Msearching scale 1 Z rot -2.3 ^Msearching scale 1 Z rot -2.0 > > ^Msearching scale 1 Z rot -1.8 > > ^Msearching scale 1 Z rot -1.5 ^Msearching scale 1 Z rot -1.3 > > ^Msearching scale 1 Z rot -1.0 ^Msearching scale 1 Z rot -0.8 > > ^Msearching scale 1 Z rot -0.5 ^Msearching scale 1 Z rot -0.3 > > ^Msearching scale 1 Z rot -0.0 ^Msearching scale 1 Z rot 0.2 > > ^Msearching scale 1 Z rot 0.5 ^Msearching scale 1 Z rot 0.7 > > ^Msearching scale 1 Z rot 1.0 ^Msearching scale 1 Z rot 1.2 > > ^Msearching scale 1 Z rot 1.5 ^Msearching scale 1 Z rot 1.7 > > ^Msearching scale 1 Z rot 2.0 ^Msearching scale 1 Z rot 2.2 > > ^Msearching scale 1 Z rot 2.5 ^Msearching scale 1 Z rot 2.7 > > ^Msearching scale 1 Z rot 3.0 ^Msearching scale 1 Z rot 3.2 > > ^Msearching scale 1 Z rot 3.5 ^Msearching scale 1 Z rot 3.7 global > > minimum found at slice 129.0, rotations (-2.52, -3.27) > > final transformation (x=129.0, yr=-2.521, zr=-3.273): > > 0.997 0.057 -0.044 -2.975; > > -0.057 0.998 0.003 -6.742; > > 0.044 -0.000 0.999 -9.547; > > 0.000 0.000 0.000 1.000; > > Segmentation fault > > > > > > Thanks > > > > > > PPJ > > --------------------------------------------------------------------- > > Pedro Paulo de Magalhães Oliveira Junior > > Netfilter & SpeedComm Telecom > > -- www.netfilter.com.br > > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > > > > > > > _______________________________________________ > > 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.
