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Just to be sure: *does* /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi exist?
Tim
On July 6, 2019 at 1:27 PM vittal korann vittalkorann@gmail.com wrote:
External Email - Use CautionHi FS experts,
I wanted to run the gyrification index for all patients with Schizophrenia and volunteers. When I entered the command: "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output
" Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02 /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy' #-------------------------------------------- #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019 /usr/local/freesurfer/subjects/SATM124/surf
mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh
nsubjects = 1 ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019
For more details, see the log file /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"
I never faced this problem before while running gyrification index. To me, it's looks bizarre. Would appreciate any help.
Thanks & regards -Korann _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany