Dear Doug, thanks for putting mri_vol2vol on the ftp site, and sorry for bothering you again with this. I did as suggested, but I still get an error, now when attempting to run xhemireg. Apparently nu.mgz is missing.
Please find the log attached. Thank you very much again, Irene Le vendredi 18 mai 2012 à 11:24 -0400, Douglas N Greve a écrit : > You'll need a new version of mri_vol2vol, which I have put on that ftp site. > doug > > On 05/18/2012 04:25 AM, Irene Altarelli wrote: > > Thanks for your help, Doug. > > > > It seems as if there is another script problem then, because when > > running the command I get the following error message (log also > > attached): > > ERROR: Option --keep-precision unknown > > > > I'm using Fs version 5, and the version of xhemireg I have downloaded > > is: v 1.22 2012/01/20 20:12:32. > > > > Should that --keep-precision option be removed from the script? > > > > Thank you, > > Irene > > > > > > > > Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit : > >> Irene, this is a problem with the script. The work-around is to run > >> xhemireg before running surfreg with the --xhemi option. > >> > >> doug > >> > >> On 05/16/2012 01:56 AM, Irene Altarelli wrote: > >>> Dear Doug, > >>> > >>> here is what I get. > >>> > >>> First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > >>> attached log file. Here is the terminal output: > >>> > >>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > >>> cd /home/ialtarelli > >>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > >>> --lh > >>> > >>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > >>> x86_64 GNU/Linux > >>> #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > >>> #CMD# mris_register -curv -annot > >>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere > >>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif > >>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > >>> using smoothwm curvature for final alignment > >>> zeroing medial wall in aparc.annot > >>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > >>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > >>> reading surface > >>> from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > >>> reading colortable from annotation file... > >>> colortable with 36 entries read > >>> (originally > >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > >>> reading template parameterization > >>> from > >>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > >>> ripping medial wall... > >>> writing registered surface > >>> to > >>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > >>> curvature mean = 0.007, std = 0.603 > >>> curvature mean = 0.030, std = 0.806 > >>> curvature mean = 0.024, std = 0.853 > >>> curvature mean = 0.009, std = 0.826 > >>> curvature mean = 0.011, std = 0.936 > >>> curvature mean = 0.003, std = 0.836 > >>> curvature mean = 0.005, std = 0.972 > >>> curvature mean = 0.001, std = 0.837 > >>> curvature mean = 0.001, std = 0.988 > >>> curvature mean = -0.032, std = 0.312 > >>> curvature mean = 0.032, std = 0.124 > >>> curvature mean = 0.079, std = 0.315 > >>> curvature mean = 0.031, std = 0.151 > >>> curvature mean = 0.049, std = 0.489 > >>> curvature mean = 0.031, std = 0.165 > >>> curvature mean = 0.028, std = 0.631 > >>> curvature mean = 0.031, std = 0.171 > >>> curvature mean = 0.011, std = 0.749 > >>> 159: 0 negative triangles > >>> surfreg-Run-Time-Hours aa_tris lh 0 0,90 > >>> mardi 15 mai 2012, 20:17:58 (UTC+0200) > >>> surfreg done > >>> > >>> Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the > >>> terminal output is just: > >>> > >>> ERROR: cannot > >>> find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere > >>> > >>> without any log file, at least I can't find any modified file in the > >>> subject's folder. > >>> > >>> > >>> Hope this helps make things clearer. > >>> Many thanks in advance! > >>> Irene > >>> > >>> > >>> Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit : > >>>> Can you send me the command line and terminal output? Did you run > >>>> xhemireg first? Should not have had to ... > >>>> > >>>> On 05/15/2012 03:02 PM, irene.altare...@ens.fr wrote: > >>>>> Dear Doug, > >>>>> > >>>>> where would that log file be? As the /subject/xhemi fails to be created > >>>>> the log > >>>>> normally appearing in there cannot be found.. Sorry if I misunderstood > >>>>> something. > >>>>> > >>>>> Thanks, > >>>>> Irene > >>>>> > >>>>> > >>>>> Selon Douglas N Greve<gr...@nmr.mgh.harvard.edu>: > >>>>> > >>>>>> Hi Irene, can you send the log file for the command that is failing? > >>>>>> doug > >>>>>> > >>>>>> On 05/15/2012 01:28 PM, Irene Altarelli wrote: > >>>>>>> Dear all, > >>>>>>> > >>>>>>> I'm trying to use the new script for the inter-hemisphere analysis, in > >>>>>>> Fs version 5.0. I have downloaded the files as suggested > >>>>>>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html). > >>>>>>> > >>>>>>> Surfreg seems to be running fine (surfreg --s subject --t > >>>>>>> fsaverage_sym > >>>>>>> --lh), but I have problems then with the --xhemi option. Some files > >>>>>>> appear to be missing, I get the following error messages: > >>>>>>> > >>>>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere > >>>>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm > >>>>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere > >>>>>>> ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot > >>>>>>> > >>>>>>> lh.fsaverage_sym.sphere.reg is created in $subject as it should > >>>>>>> (please > >>>>>>> find the surfreg log below). > >>>>>>> > >>>>>>> Thank you in advance, > >>>>>>> Irene > >>>>>>> > >>>>>>> > >>>>>>> Log file for surfreg > >>>>>>> samedi 12 mai 2012, 17:36:31 (UTC+0200) > >>>>>>> > >>>>>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > >>>>>>> cd /home/ialtarelli > >>>>>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym > >>>>>>> --lh > >>>>>>> > >>>>>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > >>>>>>> x86_64 GNU/Linux > >>>>>>> #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) > >>>>>>> #CMD# mris_register -curv -annot > >>>>>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere > >>>>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif > >>>>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg > >>>>>>> using smoothwm curvature for final alignment > >>>>>>> zeroing medial wall in aparc.annot > >>>>>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > >>>>>>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > >>>>>>> reading surface > >>>>>>> from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... > >>>>>>> reading colortable from annotation file... > >>>>>>> colortable with 36 entries read > >>>>>>> (originally > >>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > >>>>>>> reading template parameterization > >>>>>>> from > >>>>>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > >>>>>>> ripping medial wall... > >>>>>>> writing registered surface > >>>>>>> to > >>>>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... > >>>>>>> curvature mean = 0.007, std = 0.603 > >>>>>>> curvature mean = 0.030, std = 0.806 > >>>>>>> curvature mean = 0.024, std = 0.853 > >>>>>>> curvature mean = 0.009, std = 0.826 > >>>>>>> curvature mean = 0.011, std = 0.936 > >>>>>>> curvature mean = 0.003, std = 0.836 > >>>>>>> curvature mean = 0.005, std = 0.972 > >>>>>>> curvature mean = 0.001, std = 0.837 > >>>>>>> curvature mean = 0.001, std = 0.988 > >>>>>>> curvature mean = -0.032, std = 0.312 > >>>>>>> curvature mean = 0.032, std = 0.124 > >>>>>>> curvature mean = 0.079, std = 0.315 > >>>>>>> curvature mean = 0.031, std = 0.151 > >>>>>>> curvature mean = 0.049, std = 0.489 > >>>>>>> curvature mean = 0.031, std = 0.165 > >>>>>>> curvature mean = 0.028, std = 0.631 > >>>>>>> curvature mean = 0.031, std = 0.171 > >>>>>>> curvature mean = 0.011, std = 0.749 > >>>>>>> 159: 0 negative triangles > >>>>>>> surfreg-Run-Time-Hours aa_copie lh 0 0,84 > >>>>>>> samedi 12 mai 2012, 18:26:49 (UTC+0200) > >>>>>>> surfreg done > >>>>>>> > >>>>>>> > >>>>>> -- > >>>>>> 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 > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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. > >>>>>> > >>>>>> > >>>>>> > > -- > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23
/home/ialtarelli/freesurfer/bin/xhemireg --s ac_copie $Id: xhemireg,v 1.22 2012/01/20 20:12:32 greve Exp $ mardi 29 mai 2012, 18:23:42 (UTC+0200) Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux /home/ialtarelli/DATABASE/Karla5/ac_copie setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ mardi 29 mai 2012, 18:23:42 (UTC+0200) mardi 29 mai 2012, 18:23:42 (UTC+0200) mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/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 /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/orig.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/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 1338519975 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/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 /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/T1.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/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 1339218149 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/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 /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/brain.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/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 1338816872 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/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 /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/brainmask.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/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 1338547514 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/norm.mgz --targ mri/norm.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/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 /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/norm.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/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 1339303630 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/aseg.mgz --targ mri/aseg.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/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 /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/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 1338957273 Resampling Output registration matrix is identity mri_vol2vol done mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz --left-right-swap-label mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz --left-right-swap-label $Id: mri_convert.c,v 1.194 2012/04/13 03:44:23 greve Exp $ reading from /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz... Performing left-right swap of labels TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aseg.mgz... mri_vol2vol --mov mri/aparc+aseg.mgz --targ mri/aparc+aseg.mgz --reg /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+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/aparc+aseg.mgz targvol mri/aparc+aseg.mgz outvol /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz regfile /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision int (1) Gdiag_no -1 Synth 0 SynthSeed 1339184551 Resampling Output registration matrix is identity mri_vol2vol done mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz --left-right-swap-label mri_convert /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz --left-right-swap-label $Id: mri_convert.c,v 1.194 2012/04/13 03:44:23 greve Exp $ reading from /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz... Performing left-right swap of labels TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/ialtarelli/DATABASE/Karla5//ac_copie/xhemi/mri/aparc+aseg.mgz... mardi 29 mai 2012, 18:24:20 (UTC+0200) recon-all -sb ac_copie/xhemi -talairach Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/ialtarelli/DATABASE/Karla5 Actual FREESURFER_HOME /home/ialtarelli/freesurfer Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux #-------------------------------------------- #@# Talairach Tue May 29 18:24:25 CEST 2012 /home/ialtarelli/DATABASE/Karla5/ac_copie/xhemi/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: input volume nu.mgz does not exist Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux recon-all -s ac_copie/xhemi exited with ERRORS at Tue May 29 18:24:26 CEST 2012
_______________________________________________ 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.
