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." <jiglesiasgonza...@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-0b5f4a8c8...@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 <ckk...@unimelb.edu.au> wrote:
>
> External Email - Use Caution
>
> Hi 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-boun...@nmr.mgh.harvard.edu on behalf of
> freesurfer-requ...@nmr.mgh.harvard.edu"
> <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> freesurfer-requ...@nmr.mgh.harvard.edu> wrote:
>
>> External email: Please exercise caution
>>
>> Send Freesurfer mailing list submissions to
>> freesurfer@nmr.mgh.harvard.edu
>>
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>> .mgh.harvard.edu
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Freesurfer digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: Hippocampal Subfields error "no such file or
>> directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.)
>> 2. Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy)
>> 3. LGI FS 7.1 (Del Re, Elisabetta)
>> 4. mri_glmfit with pvr (std...@virgilio.it)
>> 5. 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." <jiglesiasgonza...@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-c916-4249-9983-557a25229...@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_m0IkJHWaqcVYgXiltKvmf2sZt9X-pyYSQmncbstu3rICy2Z7fHggRXk-aKCs7Fr-HTjpj0zQ6tCKLBMJ8qQlxpHWzL3Pl8OR-xTpN-F23znGzhgWE7K9yMHxIKC4JDu_uhiU4UqXswGp7DW6ImpICnIp2rAN9sjKc2johSTK9aRjCmaxJgCb5oKn4sJyy6IbRQBmyVceflyPgKIXagCBaIcBUNYGwHkmdx9RCUleJuy7MjerHcAPxmXS2QZAAA/http%3A%2F%2Fwww.jeiglesias.com
>> s.com
>>
>>> On Jun 9, 2021, at 00:23, Chester Kang <ckk...@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/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
>>>
>>> ..."
>>>
>>>
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