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
