Re: [Freesurfer] mris_topo_fixer -mgz -warnings -seed 1234

2012-10-24 Thread Anne Uhlmann
d to your artifact, but the new one will at least complete and produce surfaces, although they may not be accurate and you might have to do some editing. cheers Bruce On Wed, 24 Oct 2012, Anne Uhlmann wrote: > Hi Bruce, > > I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.

Re: [Freesurfer] mris_topo_fixer -mgz -warnings -seed 1234

2012-10-24 Thread Anne Uhlmann
Fischl 24/10/2012 13:42 >>> Hi Anne can you cc the list so others can answer? What version are you running? This is something we fixed a while ago cheers Bruce On Wed, 24 Oct 2012, Anne Uhlmann wrote: > Hi Bruce, > > Sorry about that. Please find the recon-all.log fi

[Freesurfer] mris_topo_fixer -mgz -warnings -seed 1234

2012-10-22 Thread Anne Uhlmann
Hi there, I am having trouble with one of my scans where the right hemisphere is not getting included in the analysis from the "Fix Topology rh" point on. This is the error message I get: Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: rec

[Freesurfer] qdec factor.levels problem

2012-07-03 Thread Anne Uhlmann
Hello FreeSurfers, I have a similar problem as described in an old thread (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12357.html) - qdec doesn't read my factor.levels properly. I have checked the files with gedit and can't see any control characters, which might have caused the

[Freesurfer] skullstrip eats brain and leaves skull

2012-05-23 Thread Anne Uhlmann
Hi Freesurfers, I have problems with the troubleshoot of a scan that didn't run at all within autorecon (while the scan actually looks good). So I ran the skullstrip manually and came across the following phenomenon: -when using waterthreshold 25 it gives me an error message and no brainmask.mgz