OK, I put a new version of xhemireg there that will create the nu.mgz. The newer version of the talairach do not need nu.mgz which is why I did not have it in the xhemireg I gave you. doug
On 06/02/2012 11:12 AM, Irene Altarelli wrote: > My command was: > xhemireg --s ac_copie > > The terminal output is identical to the log file (attached), ending by: > > #@# 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 > > > > Should I skip that by using the --no-tal flag? > Thanks! > Irene > > > Le samedi 02 juin 2012 à 10:57 -0400, Douglas Greve a écrit : >> Can you send your cmd and terminal output? >> doug >> >> On 6/2/12 9:46 AM, Irene Altarelli wrote: >>> 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 >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
