Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage folder to the SUBJECT_DIR folder and run recon-all … -qcache it will go through. But I think something is missing because in the surf folder, there are no *h.pial.outer_smoothed files created. I really need the files to go forward. Thanks.
Reporting on 70 segmentations Using PrintSegStat mri_segstats done /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/label INFO: fsaverage subject does not have uptodate *rhinal labels! \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 27 02:44:34 PST 2018 \n mri_label2label --srcsubject fsaverage --srclabel /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject SHICEP_S15_84_KG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n No such file or directory mri_label2label.bin: could not open label file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label
srclabel = /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SHICEP_S15_84_KG trglabel = ./lh.BA1_exvivo.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 /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label Darwin Lin.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64
recon-all -s SHICEP_S15_84_KG exited with ERRORS at Tue Feb 27 02:44:34 PST 2018
For more details, see the log file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting