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. > >>>> > >>>> > >>>> > >>> > -- 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 aa_tris $Id: xhemireg,v 1.22 2012/01/20 20:12:32 greve Exp $ vendredi 18 mai 2012, 10:19:02 (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/aa_tris setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ vendredi 18 mai 2012, 10:19:02 (UTC+0200) vendredi 18 mai 2012, 10:19:02 (UTC+0200) mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/lrrev.register.dat --o /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/mri/orig.mgz --keep-precision --no-save-reg
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