Dear Chester, What command did you exactly run? There seems to be a mix of T1 and T1+additionalMRI segmentation commands in there. Cheers, /Eugenio

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

On Jun 9, 2021, at 00:23, Chester Kang ckkang@unimelb.edu.au wrote:

   External Email - Use Caution        

Hello FreeSurfer Developers,

I am trying to run subfield segmentation of the hippocampus using Freesurfer v7.1.0. Recon-all has been previously run on all subjects, however with a different version of Freesurfer (v5.3.0).

Getting the error(s): "No such file or directory" and on further investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib"

I've searched the archive but could not find a solution.

Could someone please help?

Below are details of the system and unsuccessful troubleshooting attempts.

Regards, Chester

FreeSurfer version: 7.1.0 Platform: Mac OS 10.13.3 hippocampal-subfields-T1.log is below:

Things that have been checked/tried or troubleshooting attempted:

• SIP protection is disabled (csrutil status shows "disabled")
• Checked that there are files and correct permissions in the "lib/gcc/lib" and the "MCRv84" folders
• tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
• checked the DYLD_LIBRARY_PATH value and run a step directly (both with "" empty value and the values below)

$ echo $DYLD_LIBRARY_PATH

.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib

$ /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML

/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML dyld: Library not loaded: @rpath/libmwlaunchermain.dylib Referenced from: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML Reason: image not found Abort trap: 6

=== hippocampal-subfields-T1.log ===

"...

USER chester HOST selma.nnf.unimelb.edu.au PROCESSID 17656 PROCESSOR x86_64 OS Darwin ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64

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freesurfer-darwin-macOS-7.1.0-20200511-813297b

setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all cd /data/netapp02/work/chester/global_pass_all /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310

#--------------------------------------------

#@# Hippocampal Subfields processing (T1) left Tue 8 Jun 2021 15:25:15 AEST

Setting up environment variables

DYLD_LIBRARY_PATH is .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue 8 Jun 2021 15:25:16 AEST

..."

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