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.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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