the new mris_topo_fixer is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/
On Wed, 2012-10-24 at 09:22 -0400, Bruce Fischl wrote: > yes, that should be fine. > > On Wed, 24 Oct 2012, Anne Uhlmann wrote: > > > OK, thank you. That would be great. > > Can I just run the new topo_fixer within my old freesurfer version? > > > > Cheers, > > Anne > > > > >>> Bruce Fischl <fis...@nmr.mgh.harvard.edu> 24/10/2012 15:15 >>> > > Hi Anne > > > > you should grab a new version of mris_topo_fixer. Nick or Zeke can post > > it for you. The problem may be related 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-v4.5.0 on a > > cluster > > > (which I access via putty). > > > It's the only scan that has some kind of a scanner artifact and that shows > > > this particular problem, therefore I thought there might be a link. > > > > > > Thanks, > > > Anne > > > > > > >>> Bruce Fischl <fis...@nmr.mgh.harvard.edu> 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 file attached. The error > > > > message given there is: ERROR: _FindFacePath: could not find path! > > > > > > > > No rh output is getting produced. > > > > When viewing the brainmask.mgz -surfs, an error message says: rh.white: > > > > could not open file. > > > > > > > > When trying to view rh.orig.nofix, the error message says: rh.pial: no > > > such > > > > file or directory. But the wm outline looks just like the lh one, very > > > > angular but otherwise no defects. Sometimes voxels are included that > > > should > > > > not be white matter and in the occipital area some of the white matter > > is > > > > excluded. > > > > > > > > I can't say much about the rh.inflated.nofix. I can only view it in > > > tkmedit > > > > and it seems to have some fine disruptions in the occipital area. > > > > > > > > Thanks for your help. > > > > Regards, Anne > > > > > > > > > > > > > > > > > > > > >>> Bruce Fischl <fis...@nmr.mgh.harvard.edu> 22/10/2012 15:50 >>> > > > > Hi Anne > > > > > > > > can you post the whole recon-all.log file? I don't think you included > > the > > > > actual error message. Also, you can look at the rh.inflated.nofix and > > > > rh.orig.nofix to see if there are any really big defects in the rh > > before > > > > fixing. Is no rh output produced? > > > > > > > > Bruce > > > > > > > > On Mon, 22 Oct 2012, Anne Uhlmann wrote: > > > > > > > > > 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: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ > > > > > /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all > > >>>PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/ > > M > > > A > > > > S11 > > > > > 2.12.1107.5.2/scripts > > > > > CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh > > > > > > > > > > The orig.mgz looks OKish (it's not great) except for some kind of a > > > > scanner > > > > > artifact in 2 slices of the scan. I tried to fix it with control > > points > > > > and > > > > > making edits to the white matter, but unfortunately it didn't solve > > the > > > > > problem. I am grateful for any suggestions. > > > > > > > > > > Thank you and best regards, > > > > > Anne > > > > > > > > > > ### > > > > > > > > > > UNIVERSITY OF CAPE TOWN > > > > > > > > > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > > > > > published on our website at > > > > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable > > from > > > > +27 > > > > > 21 650 9111. This e-mail is intended only for the person(s) to whom it > > > is > > > > > addressed. If the e-mail has reached you in error, please notify the > > > > author. > > > > > If you are not the intended recipient of the e-mail you may not use, > > > > > disclose, copy, redirect or print the content. 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