External Email - Use Caution Hello FreeSurfer users,
I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory called MCRv80 in my FREESURFER_HOME. The first error says kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. Does anything seem incorrect? My path looks like this: /data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:. MatlabRuntime - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime> surfer.nmr.mgh.harvard.edu Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 6.0 and the development version require the Matlab R2012b (v8.0) runtime (note that development versions from January 2018 onwards require the Matlab R2014b - v8.4 - runtime instead). ERROR MESSAGE: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Aug 21 13:45:43 PDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlApplyTransform: line 3: kvlApplyTransform.bin: command not found mv: cannot stat ‘imageDump_transformed.mgz’: No such file or directory /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_right//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging
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