External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez,
Eugenio <e.igles...@ucl.ac.uk>
Sent: Tuesday, August 21, 2018 3:17:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield segmentation
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Nillo, Ryan Michael R
<ryanmichael.ni...@ucsf.edu>
Sent: Tuesday, August 21, 2018 9:58:25 PM
To: Freesurfer support list
Subject: [Freesurfer] hippocampal subfield segmentation
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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