what version of FS are you using?
On 02/27/2018 01:29 PM, shilin18 wrote:
*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. *
Also, are there ways to manually generate *h.pial-outer-smoothed and other related files, so as to accomplish the final step for iElvis if the *h.pial-outer-smoothed files and a bunch of *h.pial* files are missing?
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
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