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:

---------------------------------------------------------------------

FREESURFER_HOME: /Applications/freesurfer_5_270218

Build stamp: freesurfer-Darwin-OSX-ElCapitan-dev-20180207-e9879ec181

Kernel info: Darwin 15.0.0 x86_64

---------------------------------------------------------------------

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'...

--------------------------------------------------------------------------

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.

--------------------------------------------------------------------------

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

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

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

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.fi> wrote:

Thank you, but what exactly should I do?

-Reetta-Liina Armio

Lähetetty iPhonesta

Fereshte <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.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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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.

_______________________________________________
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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.