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.Altarelli@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 Grevegreve@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 >> greve@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 greve@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
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