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_10000_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_10000_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 $* > *hemi = rh* > *srcid = > ./PALM_results/rh_thickness_n34_10000_PALM_tfce_tstat_fwep.mgz* > *srcsubjid = fsaverage* > *srcsurf = white* > *srcframe = 0* > *thsign = pos* > *thmin = 0.99* > *thmax = -1* > *fdr = -1* > *minarea = 0* > *xfmfile = talairach.xfm* > *nth = -1* > *subjectsdir = /media/Data/PEH/NEW_FS_analysis* > *FixMNI = 1* > *------------- XFM matrix (RAS2RAS) ---------------* > */media/Data/PEH/NEW_FS_analysis/fsaverage/mri/transforms/talairach.xfm* > * 1.00000 0.00000 0.00000 0.00000;* > * 0.00000 1.00000 0.00000 0.00000;* > * 0.00000 0.00000 1.00000 0.00000;* > * 0.00000 0.00000 0.00000 1.00000;* > *----------------------------------------------------* > *Reading source surface > /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* > *MRISread(): could not open file* > *No such file or directory* > *mri_surfcluster: could not read surface > /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white* > *No such file or directory* > > *>$ 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
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