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.
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.
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.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas Greve -
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Irene Altarelli