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Hi Juan,

Thank you for the quick reply. I tried unsetting my PATH and LD_LIBRARY_PATH, butI am still getting the kvlAutoCrop error:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlApplyTransform: line 3: kvlApplyTransform.bin: command not found.

Full Error Message:

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 /data/sugrue2/MTS Actual FREESURFER_HOME /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0 -rw-rw----. 1 dcuneo sdl 9801677 Aug 21 16:35 /data/sugrue2/MTS/sub_0006_T1_20160920_1723/scripts/recon-all.log Linux andaman.radiology.ucsf.edu 3.10.0-862.9.1.el7.x86_64 #1 SMP Wed Jun 27 04:30:39 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0 Previous: /working/sdl_analysis/software/freesurfer6/freesurfer ‘/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin/recon-all’ -> ‘/data/sugrue2/MTS/sub_0006_T1_20160920_1723/scripts/recon-all.local-copy’ #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 16:43:12 PDT 2018

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin/segmentSF_T1.sh /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80 /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0 sub_0006_T1_20160920_1723 /data/sugrue2/MTS left

See log file: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/runtime/glnxa64:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/bin/glnxa64:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/os/glnxa64:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Warning: Name is nonexistent or not a directory: /working/sdl_analysis/software/suit Registering imageDump.mgz to hippocampal mask from ASEG /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/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 16:43:26 PDT 2018

/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin/segmentSF_T1.sh /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80 /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0 sub_0006_T1_20160920_1723 /data/sugrue2/MTS right

See log file: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/runtime/glnxa64:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/bin/glnxa64:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/os/glnxa64:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Warning: Name is nonexistent or not a directory: /working/sdl_analysis/software/suit Registering imageDump.mgz to hippocampal mask from ASEG /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlApplyTransform: line 3: kvlApplyTransform.bin: command not found mv: cannot stat ‘imageDump_transformed.mgz’: No such file or directory /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/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

Started at Tue Aug 21 16:43:10 PDT 2018 Ended at Tue Aug 21 16:43:39 PDT 2018 #@#%# recon-all-run-time-hours 0.008 recon-all -s sub_0006_T1_20160920_1723 finished without error at Tue Aug 21 16:43:39 PDT 2018 done

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Sent: Tuesday, August 21, 2018 3:17:15 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation

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Hi Ryan,

Is it possible that you're mixing versions of FreeSurfer in your PATH and/or LD_LIBRARY_PATH? Maybe you could try unsetting them before you source FreeSurfer?

Cheers,

/Eugenio

Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nillo, Ryan Michael R RyanMichael.Nillo@ucsf.edu Sent: Tuesday, August 21, 2018 9:58:25 PM To: Freesurfer support list Subject: [Freesurfer] hippocampal subfield segmentation

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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 Wikihttps://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