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 <subjid> -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 <gr...@nmr.mgh.harvard.edu> > 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 <subjid> -vno-check does not find any > > problems. It says everything is verified and checks out ok. > > > > 2) Running recon-all -s <subjid> -make all returns the message: make: > > Nothing to be done for `all'. > > > > But when I try recon-all -s <subjid> -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 Laboratorio de Imagen Médica U.M.C.E. Hospital General Universitario Gregorio Marañón Dr Esquerdo 46, 28007 Madrid, Spain Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 e-mail:jna...@hggm.es http://image.hggm.es
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