Try it with nicks control point-fixed recon-all and see if it works better
On Nov 27, 2012, at 10:44 PM, Hugh Pemberton <hughpembert...@gmail.com> wrote: > 5.1.0 > > > > On 28 November 2012 13:59, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > What version are you running? > > > > On Nov 27, 2012, at 8:51 PM, Hugh Pemberton <hughpembert...@gmail.com> wrote: > >> Generally about 4 or 5 slices away, no other images unfortunately! Any ideas >> or is the atrophy just too great? >> >> Also meant to ask about another control point based issue I've had - >> occasionally, if I've added a few to the temporal lobes because only a small >> amount has been left out and then run autorecon2 and autorecon3 the result >> is just a load more of the temporal lobe being left out, I've attached >> another couple of screen shots, in this example there's about 20 slices of >> left out matter. >> >> Cheers, >> Hugh >> >> >> On 28 November 2012 12:34, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Hugh >> >> how far is the closest visible white matter? Do you have any other image >> types (e.g. a FLAIR)? >> >> Bruce >> >> >> On Wed, 28 Nov 2012, Hugh Pemberton wrote: >> >> Hi freesurfers, >> Just want to ask how I might go about including parts of the temporal lobes >> that have been left out of the the surfaces due to severe atrophy but where >> there's no white matter so control points are of no use? I have attached a >> jpg few screen shots as examples.. >> >> Cheers, >> Hugh >> >> >> On 21 November 2012 11:29, Hugh Pemberton <hughpembert...@gmail.com> wrote: >> Hi Bruce, >> Just to let you know the new mris_topo_fixer worked and there was no >> error with the recon. >> >> I also meant to ask how I might go about including parts of the >> temporal lobes that have been left out of the the surfaces due to >> severe atrophy but where there's no white matter so control points are >> of no use? I have attached a jpg few screen shots as examples.. >> >> Cheers, >> Hugh >> >> >> On 16 November 2012 14:44, Hugh Pemberton <hughpembert...@gmail.com> >> wrote: >> Hi Bruce, >> I also meant to ask how I might go about including parts of the >> temporal lobes that have been left out of the the surfaces due >> to severe atrophy but where there's no white matter so control >> points are of no use? I have attached a few screen shots as >> examples.. >> >> Cheers, >> Hugh >> >> >> On 16 November 2012 11:14, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> this is a bug in the topology fixer. Maybe Zeke or >> Nick can post a new version of it? Was it >> mris_topo_fixer that was runing or >> mris_fix_topology? >> On Fri, 16 Nov 2012, Hugh Pemberton wrote: >> >> Hi Bruce, >> Thanks for getting back to me. In >> terminal window it says >> "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" >> but recon-all -version >> give me "$Id: recon-all,v 1.379.2.17 >> 2011/05/20 22:48:18 nicks Exp $" >> >> Hugh >> >> >> On 16 November 2012 11:05, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Hugh >> This is fixed in the newest version. >> What version are you running? >> Bruce >> >> >> >> On Nov 15, 2012, at 6:48 PM, Hugh >> Pemberton <hughpembert...@gmail.com> >> wrote: >> >> Hi, >> I have just received this error after a >> recon-all subjid- ___ >> all : >> >> ERROR: _FindFacePath: could not find >> path! >> /home/hughp/freesurfer/subjects/B______________/scripts >> >> mris_remove_intersection >> ../surf/lh.orig ../surf/lh.orig >> >> intersection removal took 0.00 hours >> removing intersecting faces >> writing corrected surface to >> ../surf/lh.orig >> >> rm ../surf/lh.inflated >> >> >> cp ../surf/lh.orig_corrected >> ../surf/lh.orig >> >> Linux naoshi-WS 3.2.0-32-generic >> #51-Ubuntu SMP Wed Sep 26 >> 21:33:09 UTC 2012 x86_64 x86_64 x86_64 >> GNU/Linux >> >> recon-all -s B______________ exited with >> ERRORS at Thu Nov 15 >> 11:40:44 EST 2012 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> Many thanks in advance, >> Best, >> Hugh >> >> >> _______________________________________________ >> 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. >> >> >> >> >> >> >> >> >> <control point error2-png.jpg> >> <Control point error-png.jpg> >
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