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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