Re: [Freesurfer] xhemi problem

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Gabriel Gonzalez Escamilla

26 Jan 2013 26 Jan '13

3:21 p.m.

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Douglas N Greve

28 Jan 28 Jan

12:18 p.m.

New subject: 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:

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)

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 * greve@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 greve@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: ggonesc@upo.es http://www.upo.es/neuroaging/es/

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/

Gabriel Gonzalez Escamilla

12:33 p.m.

New subject: xhemi problem

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freesurfer@nmr.mgh.harvard.edu

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Douglas N Greve
Gabriel Gonzalez Escamilla