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* <fjnavas2@gmail.com mailto:fjnavas2@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 ($SUBJECTS_DIR/fsaverage/surf/rh.white) exists and I can open it with freeview. The mri_surfcluster worked well in the past. However, I recently downloaded the fspalm and the mri_surfcluster attached for the fspalm. I do not know if it could interfere...??
I'm using Ubuntu 18.04 x86_64
El mié., 24 abr. 2019 a las 19:13, Greve, Douglas N.,Ph.D. (<DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>) escribió:
The "locale" error is probably not a problem. Does *//media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white exist? What operating system are you using?/* On 4/24/2019 6:41 AM, Javier Navas wrote:External Email - Use Caution Dear freesurfer experts, I want to create an annot from the output of PALM, the vertexwise file corrected by TFCE-FWEp. The values of this files are in 'p-values'. However, the mri_surfcluster has some problems: it could not recognize the fsaverage and it shows a problem with the 'locale' also. I have permissions of 'write' and 'read' in the fsaverage folder. I use the last dev version,but also it occurs with the stable version of FS 6.0. I send you the command, with the outputs and the errors. />$ 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:jnavas@hggm.es <mailto:e-mail%3Ajnavas@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:jnavas@hggm.es mailto:e-mail%3Ajnavas@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:jnavas@hggm.es mailto:e-mail%3Ajnavas@hggm.es http://image.hggm.es
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D.