But, always the first one ends properly
surfreg --s c_003 --t fsaverage_sym --lh
it's the second one that have two different errors:
surfreg --s c_003 --t fsaverage_sym --lh --xhemi
And 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,
Gabriel
El 28/01/13, Douglas N Greve <gr...@nmr.mgh.harvard.edu> 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.
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
>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/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
>tal 0
>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 0.000 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/norm.mgz --targ mri/norm.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/norm.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/norm.mgz
>targvol mri/norm.mgz
>outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/norm.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 1359823654
>
>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/aseg.mgz --targ mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/c_003/xhemi/lrrev.register.dat --o /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.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/aseg.mgz
>targvol mri/aseg.mgz
>outvol /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.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 1360101198
>
>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_convert /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.mgz /root/trabajo/freesurfer/subjects/c_003/xhemi/mri/aseg.mgz --left-right-swap-label
>mri_convert: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by mri_convert)
>
>
>
>2) When I do reboot the computer and execute just the second one:
>surfreg --s c_003 --t fsaverage_sym --lh --xhemi
>sáb ene 26 19:30:39 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
>#@# lh sáb ene 26 19:30:39 CET 2013
>#CMD# mris_register -curv -annot aparc.annot /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere /root/trabajo/freesurfer/subjects/fsaverage_sym/lh.reg.template.tif /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.fsaverage_sym.sphere.reg
>using smoothwm curvature for final alignment
>zeroing medial wall in aparc.annot
>$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
>reading surface from /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere...
>MRISread(/root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere): could not open file
>No such file or directory
>mris_register: could not read surface file /root/trabajo/freesurfer/subjects/c_003/xhemi/surf/lh.sphere
>No such file or directory
>
>
>
>
>
>El 25/01/13, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> escribió:
>>
>>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.
>>
>
>--
>--------------------------
>PhD. student Gabriel González-Escamilla
>Laboratory of Functional Neuroscience
>Department of Physiology, Anatomy, and Cell Biology
>University Pablo de Olavide
>Ctra. de Utrera, Km.1
>41013 - Seville
>- Spain -
>
>Email: ggon...@upo.es
>http://www.upo.es/neuroaging/es/
--
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/
--
--------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -
Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/
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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.
