Re: [Freesurfer] Inter-hemispheric registration issue
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
Re: [Freesurfer] Inter-hemispheric registration issue
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 Grevegr...@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
Re: [Freesurfer] Inter-hemispheric registration issue
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 Grevegr...@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:
Re: [Freesurfer] Inter-hemispheric registration issue
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
Re: [Freesurfer] Inter-hemispheric registration issue
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 Grevegr...@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
Re: [Freesurfer] Inter-hemispheric registration issue
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 Grevegr...@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
[Freesurfer] Inter-hemispheric registration issue
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 -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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.
Re: [Freesurfer] Inter-hemispheric registration issue
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.
