Re: [Freesurfer] xhemi problem
Well there is actually two kinds of error:1) when I run surfreg --s c_003 --t fsaverage_sym --lhand then:surfreg --s c_003 --t fsaverage_sym --lh --xhemi sáb ene 26 21:09:21 CET 2013 setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjects cd /root /root/trabajo/freesurfer/bin/surfreg --s c_003 --t fsaverage_sym --lh --xhemi Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux xhemi does not exist for c_003, running now xhemireg --s c_003 outdir is /root/trabajo/freesurfer/subjects/c_003/xhemi Logfile is /root/trabajo/freesurfer/subjects/c_003/xhemi/xhemireg.lh.log /root/trabajo/freesurfer/bin/xhemireg --s c_003 $Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $ sáb ene 26 21:09:21 CET 2013 Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux /root/trabajo/freesurfer/subjects/c_003 setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjects sáb ene 26 21:09:21 CET 2013 sáb ene 26 21:09:21 CET 2013 mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/orig.mgz targvol mri/orig.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/orig.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1360182876 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/T1.mgz targvol mri/T1.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/T1.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1359747149 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/brain.mgz targvol mri/brain.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brain.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1359336383 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: -1.000 0.000 0.000 255.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brainmask.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/brainmask.mgz targvol mri/brainmask.mgz outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/brainmask.mgz regfile /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat invert 0 tal0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1359564422 Final tkRAS-to-tkRAS Matrix is: -1.000 0.000
Re: [Freesurfer] problem with qdec in full install of 5.2 beta
Hello Carl, Some of the freesurfer GUIs require XQuartz. Unfortunately, XQuartz is no longer installed by default on Mac 10.8. You can download and install XQuartz from here: http://xquartz.macosforge.org/landing/ -Zeke Dear Freesurfer, When trying to start qdec I get the following error: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin Reason: image not found Trace/BPT trap Any suggestions for a work around? Thanks, Carl -- â¢~~â¢~~â¢~~â¢~~â¢~~â¢~~â¢~~⢠Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu â¢~~â¢~~â¢~~â¢~~â¢~~â¢~~â¢~~⢠___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
