5.1.0On 28 November 2012 13:59, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
What version are you running?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,HughOn 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>