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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