You’re missing your license file. https://surfer.nmr.mgh.harvard.edu/fswiki/License
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reetta-Liina Armio reetta-liina.armio@utu.fi Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 27 February 2018 at 18:35 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Invalid MEX file - FS dev-version error?
Hi!
The problem changed a bit since I downloaded the Matlab runtime compiler 2014b as the Freesurfer suggested.
See the problem below.
Here are the details:
Bugr:
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FREESURFER_HOME: /Applications/freesurfer_5_270218
Build stamp: freesurfer-Darwin-OSX-ElCapitan-dev-20180207-e9879ec181
Kernel info: Darwin 15.0.0 x86_64
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Please include the following additional information in your report:
1) subject name
2) the entire command-line executed:
This is my recons.sh file:
#!/bin/bash export FREESURFER_HOME=/Applications/freesurfer_5_270218 source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR cd $SUBJECTS_DIR segmentHA_T1.sh P04
When running the recons.sh file:
Psykiatrian-iMac:ScriptsT1_TESTI psykiatria$ bash recons.sh
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Tue Feb 27 20:27:40 EET 2018
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer_5_270218/MCRv84//runtime/maci64:/Applications/freesurfer_5_270218/MCRv84//bin/maci64:/Applications/freesurfer_5_270218/MCRv84//sys/os/maci64:/Applications/freesurfer_5_270218/lib/gcc/lib:
Registering imageDump.mgz to hippocampal mask from ASEG
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
--mov: Using imageDump.mgz as movable/source volume.
--dst: Using /Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR/P04/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz !
--sat: Using saturation 50 in M-estimator!
reading source 'imageDump.mgz'...
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ERROR: FreeSurfer license file /Applications/freesurfer_5_270218/.license not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
A path to an alternative license file can also be
specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------
/Applications/freesurfer_5_270218/bin//mri_robust_register --mov imageDump.mgz --dst /Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR/P04/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Signal 127
mv: imageDump_coregistered.mgz: No such file or directory
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
--mov: Using imageDump.mgz as movable/source volume.
--dst: Using /Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR/P04/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz !
--affine: Enableing affine transform!
--sat: Using saturation 50 in M-estimator!
reading source 'imageDump.mgz'...
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /Applications/freesurfer_5_270218/.license not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
A path to an alternative license file can also be
specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------
/Applications/freesurfer_5_270218/bin//mri_robust_register --mov imageDump.mgz --dst /Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR/P04/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --affine --sat 50: Signal 127
mv: imageDump_coregistered.mgz: No such file or directory
Reading contexts of file /Applications/freesurfer_5_270218/average/HippoSF/atlas/compressionLookupTable.txt
Constructing image-to-world transform from header information (asegModCHA.mgz)
Constructing image-to-world transform from header information (/Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR/P04/tmp/hippoSF_T1_v21_left/imageDump.mgz)
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Transforming points
Reading contexts of file /Applications/freesurfer_5_270218/average/HippoSF/atlas/compressionLookupTable.txt
--------------
Making Left-Cerebral-Cortex map to reduced label 1
Making alveus map to reduced label 1
Making subiculum-body map to reduced label 1
Making subiculum-head map to reduced label 1
Making Hippocampal_tail map to reduced label 1
Making molecular_layer_HP-body map to reduced label 1
Making molecular_layer_HP-head map to reduced label 1
Making GC-ML-DG-body map to reduced label 1
Making GC-ML-DG-head map to reduced label 1
Making CA4-body map to reduced label 1
Making CA4-head map to reduced label 1
Making CA1-body map to reduced label 1
Making CA1-head map to reduced label 1
Making CA3-body map to reduced label 1
Making CA3-head map to reduced label 1
Making HATA map to reduced label 1
Making fimbria map to reduced label 1
Making presubiculum-body map to reduced label 1
Making presubiculum-head map to reduced label 1
Making parasubiculum map to reduced label 1
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--------------
Making Left-Cerebral-White-Matter map to reduced label 2
--------------
Making Left-Lateral-Ventricle map to reduced label 3
--------------
Making Left-choroid-plexus map to reduced label 4
--------------
Making hippocampal-fissure map to reduced label 5
Making Unknown map to reduced label 5
--------------
Making Left-VentralDC map to reduced label 6
--------------
Making Left-Putamen map to reduced label 7
--------------
Making Left-Pallidum map to reduced label 8
--------------
Making Left-Thalamus-Proper map to reduced label 9
--------------
Making Left-Accumbens-area map to reduced label 10
--------------
Making Left-Caudate map to reduced label 11
Smoothing mesh collection with kernel size 3.000000 ...Smoothing class: 0
Smoothing class: 1
Smoothing class: 2
Smoothing class: 3
Smoothing class: 4
Smoothing class: 5
Smoothing class: 6
Smoothing class: 7
Smoothing class: 8
Smoothing class: 9
Smoothing class: 10
done
numberOfContrasts = 1
Image: 4
AtlasMeshToIntensityImage
1
0.398942
SLIDING
L-BFGS
Verbose: 0
MaximalDeformationStopCriterion: 1e-10
LineSearchMaximalDeformationIntervalStopCriterion: 1e-10
MaximumNumberOfIterations: 1000
BFGS-MaximumMemoryLength: 12
Resolution 1, iteration 1
Did one deformation step of max. 3.1743e-06 voxels in 0.71052 seconds
minLogLikelihoodTimesPrior =
9.5679e+05
Resolution 1, iteration 2
Did one deformation step of max. 0 voxels in 0.71766 seconds
minLogLikelihoodTimesPrior =
9.5679e+05
Smoothing mesh collection with kernel size 2.000000 ...Smoothing class: 0
Smoothing class: 1
Smoothing class: 2
Smoothing class: 3
Smoothing class: 4
Smoothing class: 5
Smoothing class: 6
Smoothing class: 7
Smoothing class: 8
Smoothing class: 9
Smoothing class: 10
done
numberOfContrasts = 1
Image: 4
AtlasMeshToIntensityImage
1
0.398942
SLIDING
L-BFGS
Verbose: 0
MaximalDeformationStopCriterion: 1e-10
LineSearchMaximalDeformationIntervalStopCriterion: 1e-10
MaximumNumberOfIterations: 1000
BFGS-MaximumMemoryLength: 12
Resolution 2, iteration 1
Did one deformation step of max. 0 voxels in 1.4062 seconds
minLogLikelihoodTimesPrior =
9.5679e+05
Fitting mesh to synthetic image from ASEG took 7.0211 seconds
Error using segmentSubjectT1_autoEstimateAlveusML (line 529)
Fitting mesh to synthetic image resulted in no deformation
Darwin Psykiatrian-iMac.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64
T1 hippocampal subfields exited with ERRORS at Tue Feb 27 20:28:06 EET 2018
For more details, see the log file /Users/psykiatria/Desktop/Reettis/Amygdala_Freesurfer_dev7_4_230118_onlyT1/SUBJECTS_DIR/P04/scripts/hippocampal-subfields-T1.log
Psykiatrian-iMac:ScriptsT1_TESTI psykiatria$
3) the error message generated:
See the hippocampal-subfields-T1.log file attached
Thank you,
Best, Reetta-Liina Armio
________________________________ Lähettäjä: Fereshte fereshte.ramezani@gmail.com Lähetetty: 27. helmikuuta 2018 18:43 Vastaanottaja: Freesurfer support list Aihe: Re: [Freesurfer] Invalid MEX file - FS dev-version error?
I’m not sure about MATLAB 2014b but you need to have installed Microsoft Visual c++ ( 2008 works fine with R2014a) and Fortran to compile MEX files; that may be the problem. Cheers
On Tue, Feb 27, 2018 at 3:42 PM Reetta-Liina Armio <rlsail@utu.fimailto:rlsail@utu.fi> wrote: Thank you, but what exactly should I do?
-Reetta-Liina Armio Lähetetty iPhonesta
Fereshte <fereshte.ramezani@gmail.commailto:fereshte.ramezani@gmail.com> kirjoitti 27.2.2018 kello 13.00: Dear Reetta Check if you’ve got the right compiler for the MEX files. Regards, Fereshte On Tue, Feb 27, 2018 at 2:10 PM Reetta-Liina Armio <rlsail@utu.fimailto:rlsail@utu.fi> wrote: Dear Freesurfer developers,
I have run basic segmentation (and hippocampal segmentation) with Freesurfer 6.0. I have now tried to run amygdala segmentation with dev-version (downloaded from the FS-site today).
I have run the same amygdalasegmentation with same platform etc in October 2017 and was able to get the volumes. I’m now trying to repeat the run with newer dev-version.
I get this Error ”invalid MEX file.”
So there is something wrong with the path?
Could you kindly help me with this?
Thank you in advance!
See log-file and Matlab-version attached.
Best, Reetta-Liina Armio
Lähetetty iPhonesta
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.