This is the command and the error line. Thanks. Stefano
recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR #-------------------------------------------- INFO: fsaverage subject does not have perirhinal labels! \n cd /Applications/freesurfer/subjects/subject_prova/Control89; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Applications/freesurfer/subjects/subject_prova/Control89; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n \n mri_label2label --srcsubject fsaverage --srclabel /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label --trgsubject SUBJECTS_DIR --trglabel ./lh.BA1.label --hemi lh -- regmethod surface \n No such file or directory mri_label2label: could not open label file /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label srclabel = /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label srcsubject = fsaverage trgsubject = SUBJECTS_DIR trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova/Control89 FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Sat Jul 9 17:20:34 CEST 2016 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Control89/SUBJECTS_DIR/scripts/recon- all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >----Messaggio originale---- >Da: "dgw" <dgwake...@gmail.com> >Data: 7-lug-2016 15.58 >A: <std...@virgilio.it>, "Freesurfer support list"<freesur...@nmr.mgh.harvard. edu> >Ogg: Re: [Freesurfer] Recon-all error after El Capitain update > >It's hard to fully diagnose, without the command you called, but it >looks like you have your SUBJECTS_DIR and SUBJECT variable wrong, and >perhaps command syntax. Take another look at your command. > >hth >d > >On Thu, Jul 7, 2016 at 2:59 AM, <std...@virgilio.it> wrote: >> Hi list, >> >> after update with El Capitain, recon-all -all produce the error reported >> below. >> >> >> Thanks >> >> srclabel = >> /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1. label >> >> srcsubject = fsaverage >> >> trgsubject = SUBJECTS_DIR >> >> trglabel = ./lh.BA1.label >> >> regmethod = surface >> >> >> srchemi = lh >> >> trghemi = lh >> >> trgsurface = white >> >> srcsurfreg = sphere.reg >> >> trgsurfreg = sphere.reg >> >> usehash = 1 >> >> Use ProjAbs = 0, 0 >> >> Use ProjFrac = 0, 0 >> >> DoPaint 0 >> >> >> SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova/subj >> >> FREESURFER_HOME /Applications/freesurfer >> >> Loading source label. >> >> No such file or directory >> >> ERROR reading >> /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh. BA1.label >> >> Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: >> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 >> >> >> recon-all -s SUBJECTS_DIR exited with ERRORS >> >> >> _______________________________________________ >> 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. >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
