Excellent, will look into it. Cheers Nick.
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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