Re: [Freesurfer] vertices don't match
Hi Doug, I have the v5.3 and the same problem in -qcache step (number of vertices do not match surface). I tried some suggestions such as "recon-all -s -vno-check"; "recon-all ..-make all"; "recon-all -s -surfvolume" and I have the same results: Error: number of vertices do not match surface. However, if I do the mris_preproc & mri_surf2surf with uncached data, I do not obtain the error and I can perform well the mri_glmfit. Is there any other option I can try to perform the analysis using the -qcache command?? Thanks in advance 2012/9/22 Douglas N Greve > Try running "recon-all -surfvolume ..." > doug > > > On 09/20/2012 02:03 PM, Darren Gitelman wrote: > > Dear List > > > > I am adding to the post on this error from yesterday regarding > > problems with running qcache. > > > > I know this has been posted to the list before, but the suggested > > fixes and checks don't fix the problem. > > > > See the error below (ERROR: number of vertices in > > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match > > surface (145332,147148) ERROR: reading curvature file) > > > > 1) Running recon-all -s -vno-check does not find any > > problems. It says everything is verified and checks out ok. > > > > 2) Running recon-all -s -make all returns the message: make: > > Nothing to be done for `all'. > > > > But when I try recon-all -s -qcache I get the error on this > > and several other subjects, but not all subjects. > > > > Checking the modification times on some files it looks like the > > thickness file came after the curv file. > > > > [drg@quser03 surf]$ ll *.thickness > > -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness > > -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness > > [drg@quser03 surf]$ ll *.curv > > -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv > > -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv > > > > Any suggestions for fixing the qcache error would be appreciated. > > > > Darren > > -- > > > > --- > > > > #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -- > > > > --- > > > > mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg > > --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval > > ./tmp.mris_preproc.6938/3300.1.mgh --sval > > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv > > --noreshape --no-cortex > > > > Source registration surface changed to sphere.reg > > > > Target registration surface changed to sphere.reg > > > > srcsubject = 3300 > > > > srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume > > > > srctype= curv > > > > trgsubject = fsaverage > > > > trgval = ./tmp.mris_preproc.6938/3300.1.mgh > > > > trgtype= > > > > srcsurfreg = sphere.reg > > > > trgsurfreg = sphere.reg > > > > srchemi= lh > > > > trghemi= lh > > > > frame = 0 > > > > fwhm-in= 0 > > > > fwhm-out = 0 > > > > label-src = (null) > > > > label-trg = (null) > > > > OKToRevFaceOrder = 1 > > > > Reading source surface reg > > /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg > > > > Loading source data > > > > Reading curvature file > > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume > > > > ERROR: number of vertices in > > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match > > surface (145332,147148) > > > > ERROR: reading curvature file > > > > Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 > > x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012 > > > > > > > > > > -- > > Darren Gitelman, MD > > Northwestern University > > 710 N. Lake Shore Dr. > > Abbott 11th Floor > > Chicago, IL 60611 > > Ph: (312) 908-8614 > > Fax: (312) 908-5073 > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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. > > -- /**\ Francisco Javier Navas Sánchez L
Re: [Freesurfer] vertices don't match
Try running "recon-all -surfvolume ..." doug On 09/20/2012 02:03 PM, Darren Gitelman wrote: > Dear List > > I am adding to the post on this error from yesterday regarding > problems with running qcache. > > I know this has been posted to the list before, but the suggested > fixes and checks don't fix the problem. > > See the error below (ERROR: number of vertices in > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match > surface (145332,147148) ERROR: reading curvature file) > > 1) Running recon-all -s -vno-check does not find any > problems. It says everything is verified and checks out ok. > > 2) Running recon-all -s -make all returns the message: make: > Nothing to be done for `all'. > > But when I try recon-all -s -qcache I get the error on this > and several other subjects, but not all subjects. > > Checking the modification times on some files it looks like the > thickness file came after the curv file. > > [drg@quser03 surf]$ ll *.thickness > -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness > -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness > [drg@quser03 surf]$ ll *.curv > -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv > -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv > > Any suggestions for fixing the qcache error would be appreciated. > > Darren > -- > > --- > > #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -- > > --- > > mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg > --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval > ./tmp.mris_preproc.6938/3300.1.mgh --sval > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv > --noreshape --no-cortex > > Source registration surface changed to sphere.reg > > Target registration surface changed to sphere.reg > > srcsubject = 3300 > > srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume > > srctype= curv > > trgsubject = fsaverage > > trgval = ./tmp.mris_preproc.6938/3300.1.mgh > > trgtype= > > srcsurfreg = sphere.reg > > trgsurfreg = sphere.reg > > srchemi= lh > > trghemi= lh > > frame = 0 > > fwhm-in= 0 > > fwhm-out = 0 > > label-src = (null) > > label-trg = (null) > > OKToRevFaceOrder = 1 > > Reading source surface reg > /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg > > Loading source data > > Reading curvature file > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume > > ERROR: number of vertices in > /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match > surface (145332,147148) > > ERROR: reading curvature file > > Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 > x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012 > > > > > -- > Darren Gitelman, MD > Northwestern University > 710 N. Lake Shore Dr. > Abbott 11th Floor > Chicago, IL 60611 > Ph: (312) 908-8614 > Fax: (312) 908-5073 > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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.
[Freesurfer] vertices don't match
Dear List I am adding to the post on this error from yesterday regarding problems with running qcache. I know this has been posted to the list before, but the suggested fixes and checks don't fix the problem. See the error below (ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file) 1) Running recon-all -s -vno-check does not find any problems. It says everything is verified and checks out ok. 2) Running recon-all -s -make all returns the message: make: Nothing to be done for `all'. But when I try recon-all -s -qcache I get the error on this and several other subjects, but not all subjects. Checking the modification times on some files it looks like the thickness file came after the curv file. [drg@quser03 surf]$ ll *.thickness -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness [drg@quser03 surf]$ ll *.curv -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv Any suggestions for fixing the qcache error would be appreciated. Darren -- --- #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -- --- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6938/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume srctype= curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6938/3300.1.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012 -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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.
