External Email - Use Caution
Hi Eugenio,
Yes, Matlab runtime had already been installed.
Copying initial description of checks/troubleshooting already done so far, "...
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)
..."
Hope to that helps!
Regards, Chester
------------------------------
Message: 4 Date: Fri, 11 Jun 2021 11:43:21 +0000 From: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded" To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: E7200246-C4B9-4198-ADEE-0B5F4A8C8C13@mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
Thanks, Chester, that looks good. Am I safely assuming that the Matlab runtime has been installed? Cheers, /Eugenio
On 10 Jun 2021, at 21:31, Chester Kang ckkang@unimelb.edu.au wrote:
External Email - Use CautionHi Eugenio,
The command that was run is segmentHA_T1.sh.
I've rerun and copy-n-pasted the entire session below.
"...
chesterk@selma:~$ source SetUpFreeSurfer_mac.sh -------- freesurfer-darwin-macOS-7.1.0-20200511-813297b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer_v7.1.0 FSFAST_HOME /Applications/freesurfer_v7.1.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/chesterk/subjects MNI_DIR /Applications/freesurfer_v7.1.0/mni FSL_DIR /usr/local/fsl_v6.0.4 chesterk@selma:~$ cd subjects chesterk@selma:~/subjects$ segmentHA_T1.sh 1001126copy #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12 AEST
Setting up environment variables
DYLD_LIBRARY_PATH is .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus ML.sh: line 33: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a pp/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 Fri 11 Jun 2021 11:25:12 AEST
For more details, see the log file /Users/chesterk/subjects/1001126copy/scripts/hippocampal-subfields-T1.log
chesterk@selma:~/subjects$ more 1001126copy/scripts/hippocampal-subfields-T1.log
USER chesterk HOST selma.nnf.unimelb.edu.au PROCESSID 37954 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
freesurfer-darwin-macOS-7.1.0-20200511-813297b
setenv SUBJECTS_DIR /Users/chesterk/subjects cd /Users/chesterk/subjects /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1001126copy
#-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12 AEST
Setting up environment variables
DYLD_LIBRARY_PATH is .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus ML.sh: line 33: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a pp/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 Fri 11 Jun 2021 11:25:12 AEST
..."
Please let me know if I can provide any other details. Thanks!
Regards, Chester
On 10/6/21, 12:51 am, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu> wrote:
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Today's Topics:
- Re: Hippocampal Subfields error "no such file or directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.)
- Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy)
- LGI FS 7.1 (Del Re, Elisabetta)
- mri_glmfit with pvr (stdp82@virgilio.it)
- Re: FW: WM or Pial edits to correct surfaces (Fischl, Bruce)
Message: 1 Date: Wed, 9 Jun 2021 12:24:19 +0000 From: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded" To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 8419D11C-C916-4249-9983-557A252291EC@mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
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://secure-web.cisco.com/1qi_706jGqyyM3M3yDYUokzl_m0IkJHWaqcVYgXiltKvmf2s... s.com
On Jun 9, 2021, at 00:23, Chester Kang ckkang@unimelb.edu.au wrote:
External Email - Use CautionHello 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/fr eesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib /gcc/lib
$ /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML dyld: Library not loaded: @rpath/libmwlaunchermain.dylib Referenced from: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus ML.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
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/fr eesurfer_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_autoEstimateAlve usML.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
..."