Dear Daniel, Is this Linux or MAC? It looks like a mix to me. Cheers, /Eugenio

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, 4 August 2019 at 15:19 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T1.sh error

External Email - Use Caution Hello,

When trying to run segmentHA_T1.sh I keep getting the following error log that I am having a lot of trouble debugging. Matlab 2014b is installed. Any help or guidance would be greatly appreciated!

------------------------------ USER dcallow HOST compute-4-9.bswift.umd.eduhttp://compute-4-9.bswift.umd.edu PROCESSID 8771 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux compute-4-9.bswift.umd.eduhttp://compute-4-9.bswift.umd.edu 2.6.32-754.15.3.el6.x86_64 #1 SMP Thu Jun 13 22:49:44 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux ------------------------------

freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc

setenv SUBJECTS_DIR /homes/dcallow/freesurfer_Tracy cd /a/ha-nfs-1-ib/export/home/bswift/dcallow /homes/dcallow/freesurfer_dev/bin/segmentHA_T1.sh HMN002

#-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Sun Aug 4 15:08:35 EDT 2019 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/homes/dcallow/freesurfer_dev/MCRv84//runtime/maci64:/homes/dcallow/freesurfer_dev/MCRv84//bin/maci64:/homes/dcallow/freesurfer_dev/MCRv84//sys/os/maci64:/hom$ /homes/dcallow/freesurfer_dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: /homes/dcallow/freesurfer_dev/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/s$ @#@FSTIME 2019:08:04:15:08:35 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 0.07 S 0.00 U 0.00 P 15% M 1360 F 0 R 2250 W 0 c 13 w 171 I 40 O 0 L 0.12 0.68 0.88 @#@FSLOADPOST 2019:08:04:15:08:35 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.12 0.68 0.88 Linux compute-4-9.bswift.umd.eduhttp://compute-4-9.bswift.umd.edu 2.6.32-754.15.3.el6.x86_64 #1 SMP Thu Jun 13 22:49:44 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Sun Aug 4 15:08:36 EDT 2019

Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298