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
