On 29 November 2012 04:58, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote:

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
> <hughpemberton1@gmail.com> wrote:
>
>
>
> > 5.1.0
> >
> >
> >
> >
> > On 28 November 2012 13:59, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> > wrote:
> > What version are you running?
> >
> >
> >
> >
> > On Nov 27, 2012, at 8:51 PM, Hugh Pemberton
> > <hughpemberton1@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
> > > <fischl@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
> > > <hughpemberton1@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
> > > <hughpemberton1@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
> > > <fischl@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
> > > <fischl@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
> > > <hughpemberton1@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
> > >
> > >
> > >
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> > >
> > >
> > > <control point error2-png.jpg>
> > > <Control point error-png.jpg>
> >
> >
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