Hugh, That fix is described in the Known Issues section of 5.1 on the Release Notes page:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes look for the section where you need to edit your recon-all script to comment-out the line where the control point is used by ca_norm. Nick On Tue, 2012-11-27 at 22:53 -0500, Bruce Fischl wrote: > 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> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
