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" dgwakeman@gmail.com Data: 7-lug-2016 15.58 A: stdp82@virgilio.it, "Freesurfer support list"<freesurfer@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, stdp82@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
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