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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If this e-mail is not related > to the business of UCT it is sent by the sender in the sender's individual > capacity. > > ### > > > ### 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. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###
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