External Email - Use Caution Dear Freesurfer Developers
I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well. It sets up the environment and then complains about myMRIread and Error in segmentSubjectT1_autoEstimateAlveusML (line 157) Here is the command line output: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is <redacted, because I’m paranoid> Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 157) @#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 33416 O 0 L 0.02 5.50 14.86 @#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.78 4.16 13.38 Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018 What am I doing wrong here? Thanks very much. Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fre...@sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
