This is pretty weird. Can you try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
On 4/24/19 2:56 PM, Javier Navas wrote: > > External Email - Use Caution > > > ---------- Forwarded message --------- > De: *Javier Navas* <fjnav...@gmail.com <mailto:fjnav...@gmail.com>> > Date: mié., 24 abr. 2019 a las 19:22 > Subject: Re: [Freesurfer] mri_surfcluster ERROR > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > Yes, the file ($SUBJECTS_DIR/fsaverage/surf/rh.white) exists and I can > open it with freeview. The mri_surfcluster worked well in the past. > However, I recently downloaded the fspalm and the mri_surfcluster > attached for the fspalm. I do not know if it could interfere...?? > > I'm using Ubuntu 18.04 x86_64 > > El mié., 24 abr. 2019 a las 19:13, Greve, Douglas N.,Ph.D. > (<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió: > > The "locale" error is probably not a problem. Does > *//media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white exist? > What operating system are you using?/* > > On 4/24/2019 6:41 AM, Javier Navas wrote: >> >> External Email - Use Caution >> >> Dear freesurfer experts, >> >> I want to create an annot from the output of PALM, the vertexwise >> file corrected by TFCE-FWEp. The values of this files are in >> 'p-values'. >> >> However, the mri_surfcluster has some problems: it could not >> recognize the fsaverage and it shows a problem with the 'locale' >> also. I have permissions of 'write' and 'read' in the fsaverage >> folder. I use the last dev version,but also it occurs with the >> stable version of FS 6.0. >> >> I send you the command, with the outputs and the errors. >> >> />$ 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 <mailto:e-mail%3ajna...@hggm.es> >> http://image.hggm.es >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:e-mail%3ajna...@hggm.es> > http://image.hggm.es > > > -- > /**********************************************************\ > 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 <mailto:e-mail%3ajna...@hggm.es> > http://image.hggm.es _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
