Re: [Freesurfer] xhemi problem
Can you send the command line and terminal output? On 01/25/2013 09:38 AM, Gabriel Gonzalez Escamilla wrote: > Dear FS experts, > > I'm trying to perform the intrerhemispheric registration method on my > centOS 4, I have downloaded all the files, but the mri_convert is > saying that does not found the necessary libraries. I did download the > mri_convert.linux, I have tried to re-download the file, but it > apparentelly is not available anymore. > > Can any one help me? > > Many thanks in advanced, > Gabriel > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
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 0.00
Re: [Freesurfer] xhemi problem
The second command is probably failing because the first command is failing. The 1st is failing because you don't have GLIBC 2.4. I'll have to leave that one for Nick or Zeke. doug On 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote: > Well there is actually two kinds of error: > > 1) when I run > surfreg --s c_003 --t fsaverage_sym --lh > > and 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/brai
Re: [Freesurfer] xhemi problem
Thanks Doug for your answerBut, always the first one ends properlysurfreg --s c_003 --t fsaverage_sym --lhit's the second one that have two different errors:surfreg --s c_003 --t fsaverage_sym --lh --xhemiAnd yes you are right, it says that it's because of the library but, the original mri_convert did't have that trouble. I have also tried to excecute the command xhemireg but didn't work either.Thanks,GabrielEl 28/01/13, Douglas N Greve escribió:The second command is probably failing because the first command is failing. The 1st is failing because you don't have GLIBC 2.4. I'll have to leave that one for Nick or Zeke.dougOn 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote:>Well there is actually two kinds of error:>>1) when I run>surfreg --s c_003 --t fsaverage_sym --lh>>and 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>tal 0>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>tal 0>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>tal 0>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/brainm
