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
..."
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Message: 2 Date: Wed, 9 Jun 2021 13:09:17 +0000 From: "Lurie, Lucy" llurie@email.unc.edu Subject: [Freesurfer] Ill-Conditioned/Badly Scaled Matrix Error To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 3BCD8EA8-8DA7-4A8A-BA82-8B7A4F2D2588@ad.unc.edu Content-Type: text/plain; charset="utf-8"
External Email - Use CautionHello
I am trying to a whole brain analysis with one group and five covariates. I am getting an error that the design matrix may be ill-conditioned or badly scaled. I checked over the fsgd file in TextEdit and it seems to be formatted correctly. I am using Freesurfer version 5.3.0 and my platform is macOS Big Sur version 11.4. I would appreciate any help further troubleshooting this error. Thank you!
ERROR: matrix is ill-conditioned or badly scaled, condno = 13065 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send:
- Your command line: mri_glmfit --y
lh.eig_cgORCE_baselineORCE_teenCG.thickness.10.mgh --fsgd eig_cgORCE_baselineORCE_teenCG.fsgd dods --C eig_cgORCE3042_slope.mtx --C eig_cgORCEbaseline_slope.mtx --C eig_teenCGqual_slope.mtx --surf fsaverage lh --cortex --glmdir lh.eig_cgORCE_baselineORCE_teenCGagesex.glmdir 2. The FSGD file (if using one) 3. And the design matrix
Design matrix ------------------ 1.000 0.000 16.660 2.950 2.200 0.000; 1.000 0.000 16.960 1.900 2.600 0.000; 1.000 0.000 17.390 2.450 2.800 0.000; 1.000 1.000 17.130 2.300 2.500 0.000; 1.000 1.000 16.980 2.400 2.300 0.000; 1.000 0.000 17.690 2.200 2.900 0.000; 1.000 1.000 16.870 2.750 2.900 1.000; 1.000 0.000 17.570 2.550 1.700 0.000; 1.000 0.000 17.130 2.150 1.928 0.000; 1.000 1.000 17.650 2.750 2.200 0.000; 1.000 1.000 17.210 2.450 2.500 1.000; 1.000 0.000 15.610 3.100 1.565 1.000; 1.000 0.000 16.440 2.650 2.300 0.000; 1.000 1.000 17.350 2.400 2.600 0.000; 1.000 0.000 16.800 1.600 1.400 0.000; 1.000 1.000 17.980 2.200 2.300 1.000; 1.000 1.000 16.890 2.800 1.600 1.000; 1.000 0.000 16.760 1.100 1.300 0.000; 1.000 1.000 16.790 2.500 1.400 0.000; 1.000 1.000 16.620 2.900 2.800 0.000; 1.000 1.000 16.500 2.500 1.200 0.000; 1.000 1.000 16.290 2.700 3.200 0.500; 1.000 0.000 16.440 3.100 2.500 1.000; 1.000 0.000 17.540 2.100 2.100 1.000; 1.000 1.000 16.810 1.900 2.600 1.000; 1.000 0.000 17.110 2.650 2.400 0.000; 1.000 1.000 16.520 2.000 2.300 0.000; 1.000 1.000 16.520 3.100 3.400 1.000; 1.000 0.000 16.320 3.300 2.800 0.500; 1.000 0.000 16.380 3.200 1.900 1.000; 1.000 0.000 16.570 2.800 2.000 0.000; 1.000 1.000 16.250 2.200 1.600 0.000; 1.000 1.000 16.820 2.900 2.600 1.000; 1.000 0.000 16.580 2.600 2.800 0.000; 1.000 1.000 16.730 2.850 3.150 0.000; 1.000 0.000 16.310 2.600 1.900 0.000; 1.000 1.000 17.010 1.700 2.400 0.000; 1.000 1.000 16.360 3.200 3.200 0.000; 1.000 1.000 16.490 2.400 1.525 0.000; 1.000 0.000 16.300 2.400 1.450 1.000; 1.000 0.000 16.060 2.200 1.300 0.000; 1.000 1.000 16.600 2.200 2.000 0.000; 1.000 0.000 16.720 3.300 2.500 0.000; 1.000 1.000 16.160 2.300 2.200 0.000; 1.000 1.000 16.140 2.800 1.850 0.000; 1.000 1.000 16.550 3.100 2.950 1.000; 1.000 1.000 17.300 3.450 2.700 1.000; 1.000 0.000 16.940 3.000 2.200 1.000; 1.000 1.000 16.550 2.700 2.850 0.000; 1.000 0.000 17.170 3.000 2.900 1.000; 1.000 0.000 17.150 2.800 2.450 0.000; 1.000 0.000 16.650 3.100 1.900 0.500; 1.000 0.000 16.070 2.700 2.900 1.000; 1.000 1.000 16.720 1.800 1.450 1.000; 1.000 0.000 16.150 2.900 1.000 0.000; 1.000 1.000 16.120 2.400 2.200 1.000; 1.000 1.000 17.540 2.600 2.600 0.000; 1.000 1.000 16.840 2.900 1.100 0.000; 1.000 1.000 15.790 3.100 1.600 1.000; 1.000 1.000 16.430 2.800 1.500 0.000; 1.000 0.000 16.390 3.300 2.700 1.000; 1.000 0.000 16.480 3.350 3.000 0.000; 1.000 1.000 16.930 3.000 1.000 0.000; 1.000 1.000 15.550 2.200 2.600 0.000; 1.000 1.000 17.080 2.900 1.500 0.000; 1.000 0.000 16.850 2.500 2.200 0.500; 1.000 1.000 16.700 2.200 1.800 0.000; 1.000 1.000 15.930 2.600 2.000 1.000; 1.000 1.000 16.080 2.600 1.200 0.500; 1.000 0.000 16.130 3.150 1.400 1.000; 1.000 1.000 16.250 3.100 1.400 1.000; 1.000 0.000 16.040 3.250 3.200 1.000; 1.000 0.000 16.040 3.500 2.900 1.000; 1.000 0.000 16.070 1.400 1.000 1.000; 1.000 0.000 16.550 3.200 2.300 1.000; 1.000 0.000 16.120 2.800 2.000 0.500; 1.000 1.000 16.450 3.150 1.400 1.000; 1.000 0.000 15.910 3.400 1.600 1.000; 1.000 1.000 15.700 3.000 2.400 1.000;
Best, Lucy Lurie (she/her/hers) Doctoral Student, Clinical Psychology Department of Psychology and Neuroscience University of North Carolina at Chapel Hill CIRCLE Labhttps://secure-web.cisco.com/18i_Rf4fzTTcqPA2OQAm3_CnM6qhNKl6D-xG6RO1PJGAuLnAlN2Qa-m8h9EZGbO9Qo7QPQAiBVNevAoHlY-jf9z7dGHxurd8Oe8uw75EoTaRxQZ_Nl1ObEe1gsWQecXmO42TYy9xWhqpijv4wchCBs6bYGaIXNVDP3iaP_YqG99OQMWqyy3Zhq6_BwSFJYIw_edeT9Drrl9CQKiDWXReHaL-jQ4DUC7cHEyRW7ZG8OXH6a9M8dPLZcaM5Lxb8KEYCKOSgtBx3kUPo_h53ZU-lOQ/https%3A%2F%2Fcirclelab.unc.edu%2F e-web.cisco.com