Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Re: Freesurfer Digest, Vol 37, Issue 15
by Sebastian Moeller 20 Mar '07

20 Mar '07

On 20. Mar 2007, at 15:46 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 8 > Date: Tue, 20 Mar 2007 15:45:25 +0100 > From: Juergen Haenggi <j.haenggi(a)psychologie.uzh.ch> > Subject: [Freesurfer] Error > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <C225B215.CE%j.haenggi(a)psychologie.uzh.ch> > Content-Type: text/plain; charset="US-ASCII" > > Dear Freesurfer users > > I am trying to run Freesurfer on a Mac, but the following error > occured: > > juergen-haenggis-computer:/Applications/freesurfer/subjects > juergenhaenggi$ > tkmedit bert orig.mgz > GLUT: Fatal Error in tkmedit.bin: could not open display: > juergen-haenggis-computer:/Applications/freesurfer/subjects > juergenhaenggi$ > It looks like you did not install and/or start X11, as far as I know (still on 10.3) there should be an additional install for X11 somewhere on the system disk (if it is not installed by default on tiger, then just start X11 before running freesurfer. It might be a good idea to start the freesurfer programs from an xterm otherwise the display error might still persist. Or add the following to you ".bashrc" # so terminal.app can start X11 applications DISPLAY=:0.0 export DISPLAY While not very clean it should do the trick and allow starting of x apps from terminal. ahoi & good luck Sebastian > I use Freesurfer v3.0.5 on Mac OS X Intel Tiger. > > Thanks a lot in advance > Best regards > Juergen > > PS: there was no solution for that problem in the archives > > ----------------------------------------------------------------------- > ---- > Juergen Haenggi, Ph.D. student > Department of Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi(a)psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > ----------------------------------------------------------------------- > ---- > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 37, Issue 15 > ****************************************** > > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

1 0

higher res recon
by David M Schnyer 20 Mar '07

20 Mar '07

Folks, We have a .7mm cubic voxel SPGR scan we would like to segment with Freesurfer. When I run it with the recon all flag -cm images retain their "native" resolution up to the normalization step of nu to T1. nu.mgz has the native resolution but T1 is converted to 256 cubic. Can I do what I want here? thanks, david -- David Schnyer, Ph.D. Imaging Research Center & Department of Psychology University of Texas, Austin tel: (512) 471-8505 fax: (512) 232-4202 http://irc.utexas.edu/index.html

2 1

Error
by Juergen Haenggi 20 Mar '07

20 Mar '07

Dear Freesurfer users I am trying to run Freesurfer on a Mac, but the following error occured: juergen-haenggis-computer:/Applications/freesurfer/subjects juergenhaenggi$ tkmedit bert orig.mgz GLUT: Fatal Error in tkmedit.bin: could not open display: juergen-haenggis-computer:/Applications/freesurfer/subjects juergenhaenggi$ I use Freesurfer v3.0.5 on Mac OS X Intel Tiger. Thanks a lot in advance Best regards Juergen PS: there was no solution for that problem in the archives --------------------------------------------------------------------------- Juergen Haenggi, Ph.D. student Department of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ---------------------------------------------------------------------------

1 0

Two problems
by Juergen Haenggi 20 Mar '07

20 Mar '07

Dear Freesurfer users I have two problems: I upgraded Freesurfer (from Linux CentOS4 v3.0.3 to v3.0.5) and recognized that the "foreach" command do not work any longer. The following error occured: ERROR: Flag -Patient03_2001 unrecognized. -Patient03_2001 -all ERROR: Flag -Patient03_2002 unrecognized. -Patient03_2002 -all The other problem concerns the selection of the tcsh shell on Mac OS X. I can change from a bash to a tcsh shell. Thanks for help in advance Best regards Juergen --------------------------------------------------------------------------- Juergen Haenggi, Ph.D. student Department of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ---------------------------------------------------------------------------

2 1

Correction
by Juergen Haenggi 20 Mar '07

20 Mar '07

Dear Freesurfer users In my former email, I meant that I can not change from bash to tcsh shell on Mac OS X. Sorry! Thanks Regards Juergen --------------------------------------------------------------------------- Juergen Haenggi, Ph.D. student Department of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ---------------------------------------------------------------------------

1 0

RE: [Freesurfer] RE: Version compatability
by Fornito, Alexander 19 Mar '07

19 Mar '07

Hi Nick, One thing I couldn't work out from the example image associated with the release notes is whether the different areas are located in the non-cortical regions of the midline. If they include cortical regions (and it appears that subgenual portions of the cingulate are) then I am interested in these areas. Ta, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

1 0

Legacy flag
by Fornito, Alexander 19 Mar '07

19 Mar '07

Hi, I was just seeking some clarification re: the legacy flag in recon-all. Can I use it on subjects procssed with older versions of Freesurfer to reconstruct surfaces that will be consistent with those generated with older versions (i.e., I can collapse data from the two versions), or is the legacy flag intended to allow new versions of recon-all to be used on old data, effectively 'updating' the surfaces (meaning they should not be analyzed together with data generated using older versions). Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

4 6

getting info from recon-all.log
by Sameer Walawalkar 16 Mar '07

16 Mar '07

Hello, My recon-all command (actually two of them) ran for some 30 hrs and 12 hours (the second one with nohup) before my windows macine rebooted. I wanted to see what was the status of the imlementation and so decided to look into the Status and Log Files. Both recon-all.log and recon-all-status.log files have the same entry given below. MNE software location set to /mnt/data/home/sameer/Software/MEGswdir/mne MATLAB software location set to /mnt/data/home/sameer/Software/MEGswdir/matl ab /mnt/data/home/sameer/Software/MEGswdir/mne/bin/mne already in PATH Note : Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly. Note : FreeSurfer environment is needed to run mne_setup_source_space This really doesn't tell me anything. Can someone please shed some light on this? thanks, sameer

2 1

Announcement: open access MR data (OASIS)
by Daniel Marcus 15 Mar '07

15 Mar '07

Dear Colleagues, The Open Access Series of Imaging Studies (OASIS) is now available at www.oasis-brains.org <http://www.oasis-brains.org/> . The data are publicly available under to a liberal Data Use Agreement available here: http://www.oasis-brains.org/app/template/UsageAgreement.vm. The first data set includes structural MR obtained from 416 subjects aged 18 to 96, including 100 subjects diagnosed with very mild to moderate Alzheimer's Disease. A longitudinal data set will be released in the coming months. A manuscript describing the project is currently in press at Journal of Cognitive Neuroscience. For more information, please visit the website. Of particular interest to this group, Bruce Fischl's group is kindly churning the whole data set through Freesurfer. The resulting goodies will be made freely available as open access data. Make sure to thank Bruce and Jenni next time you see them. Regards, Dan Marcus dmarcus(a)wustl.edu Neuroinformatics Research Group Washington University School of Medicine http://nrg.wustl.edu <http://nrg.wustl.edu/>

2 1

importing cartesian coordinates file
by abel cruz vadell 14 Mar '07

14 Mar '07

Hi everyone Could I import in FreeSurfer (specifically in TKSurfer) a cartesian coordinates files? I need to locate the position of my EEG electrodes (previously translated to the brain and each one containing the information of one hemisphere) into the surfaces generated in FreeSurfer (orig and inflated). Is there any registration tool in FreeSurfer to do that? Or any other way? Thanks ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer