Re: [Freesurfer] mri_surfcluster ERROR
External Email - Use Caution Yes, the file ($SUBJECTS_DIR/fsaverage/surf/rh.white) exists and I can open it with freeview. The mri_surfcluster worked well in the past. However, I recently downloaded the fspalm and the mri_surfcluster attached for the fspalm. I do not know if it could interfere...?? I'm using Ubuntu 18.04 x86_64 El mié., 24 abr. 2019 a las 19:13, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escribió: > The "locale" error is probably not a problem. Does > */media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white > exist? What operating system are you using?* > > On 4/24/2019 6:41 AM, Javier Navas wrote: > > External Email - Use Caution > Dear freesurfer experts, > > I want to create an annot from the output of PALM, the vertexwise file > corrected by TFCE-FWEp. The values of this files are in 'p-values'. > > However, the mri_surfcluster has some problems: it could not recognize the > fsaverage and it shows a problem with the 'locale' also. I have permissions > of 'write' and 'read' in the fsaverage folder. I use the last dev > version,but also it occurs with the stable version of FS 6.0. > > I send you the command, with the outputs and the errors. > > *>$ mri_surfcluster --in > ./PALM_results/rh_thickness_n34_1_PALM_tfce_tstat_fwep.mgz --thmin 0.99 > --hemi rh --subject fsaverage --sign pos --surf white --oannot > /media/Data/PEH/NEW_FS_analysis/PALM_results/rh_thickness_n34_1_PALM_tfce_tstat_fwep.annot* > *Could not set locale* > *No such file or directory* > *Could not set locale* > *thsign = pos, id = 1* > *version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $* > *hemi = rh* > *srcid = > ./PALM_results/rh_thickness_n34_1_PALM_tfce_tstat_fwep.mgz* > *srcsubjid = fsaverage* > *srcsurf= white* > *srcframe = 0* > *thsign = pos* > *thmin = 0.99* > *thmax = -1* > *fdr= -1* > *minarea= 0* > *xfmfile= talairach.xfm* > *nth = -1* > *subjectsdir= /media/Data/PEH/NEW_FS_analysis* > *FixMNI = 1* > *- XFM matrix (RAS2RAS) ---* > */media/Data/PEH/NEW_FS_analysis/fsaverage/mri/transforms/talairach.xfm* > * 1.0 0.0 0.0 0.0;* > * 0.0 1.0 0.0 0.0;* > * 0.0 0.0 1.0 0.0;* > * 0.0 0.0 0.0 1.0;* > ** > *Reading source surface > /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* > *MRISread(): could not open file* > *No such file or directory* > *mri_surfcluster: could not read surface > /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* > *No such file or directory* > > *>$ more error.log* > *Could not set locale* > *MRISread(): could not open file* > > Thank you in advance > -- > /**\ > 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 > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- /**\ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_surfcluster ERROR
External Email - Use Caution Dear freesurfer experts, I want to create an annot from the output of PALM, the vertexwise file corrected by TFCE-FWEp. The values of this files are in 'p-values'. However, the mri_surfcluster has some problems: it could not recognize the fsaverage and it shows a problem with the 'locale' also. I have permissions of 'write' and 'read' in the fsaverage folder. I use the last dev version,but also it occurs with the stable version of FS 6.0. I send you the command, with the outputs and the errors. *>$ mri_surfcluster --in ./PALM_results/rh_thickness_n34_1_PALM_tfce_tstat_fwep.mgz --thmin 0.99 --hemi rh --subject fsaverage --sign pos --surf white --oannot /media/Data/PEH/NEW_FS_analysis/PALM_results/rh_thickness_n34_1_PALM_tfce_tstat_fwep.annot* *Could not set locale* *No such file or directory* *Could not set locale* *thsign = pos, id = 1* *version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $* *hemi = rh* *srcid = ./PALM_results/rh_thickness_n34_1_PALM_tfce_tstat_fwep.mgz* *srcsubjid = fsaverage* *srcsurf= white* *srcframe = 0* *thsign = pos* *thmin = 0.99* *thmax = -1* *fdr= -1* *minarea= 0* *xfmfile= talairach.xfm* *nth = -1* *subjectsdir= /media/Data/PEH/NEW_FS_analysis* *FixMNI = 1* *- XFM matrix (RAS2RAS) ---* */media/Data/PEH/NEW_FS_analysis/fsaverage/mri/transforms/talairach.xfm* * 1.0 0.0 0.0 0.0;* * 0.0 1.0 0.0 0.0;* * 0.0 0.0 1.0 0.0;* * 0.0 0.0 0.0 1.0;* ** *Reading source surface /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* *MRISread(): could not open file* *No such file or directory* *mri_surfcluster: could not read surface /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* *No such file or directory* *>$ more error.log* *Could not set locale* *MRISread(): could not open file* Thank you in advance -- /******\ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: surfe
