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Hi Eugenio,

I have downloaded the most recent dev version ( freesurfer-darwin-OSX-ElCapitan-dev.tar.gz ) from here  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and I get the same error.

My version of Mac is Mac OS High Sierra Version 10.13.3


Fitting mesh to image data mask took 683.6633 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
INFO: dst volume info differs from the one stored in lta.  gets modified now.
volume geometry:
extent  : (691, 691, 473)
voxel   : ( 0.3333,  0.3333,  0.3333)
x_(ras) : ( 0.0000, -1.0000,  0.0000)
y_(ras) : (-0.0047,  0.0000,  1.0000)
z_(ras) : ( 1.0000,  0.0000,  0.0047)
c_(ras) : ( 4.2397, 13.6233, 12.2196)
file    : T2isotropic.mgz
volume geometry:
extent  : (640, 640, 225)
voxel   : ( 0.3594,  0.3594,  0.7000)
x_(ras) : ( 0.0000, -1.0000,  0.0000)
y_(ras) : (-0.0047,  0.0000,  1.0000)
z_(ras) : ( 1.0000,  0.0000,  0.0047)
c_(ras) : ( 4.2397, 13.6234, 12.2196)
file    : /Applications/freesurfer/subjects/5095/mri/orig/T2.nii
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)



MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35 CEST

For more details, see the log file /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log






What could be the problem?


Thanks in advance,

Best wishes,


El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (<e.iglesias@ucl.ac.uk>) escribió:

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Hi Miguel Angel,

This bug was recently fixed in the dev version. If you download the most recent one, you won’t have this problem.

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 13 September 2018 at 21:12
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal-Amygdala subfields error

 

        External Email - Use Caution        

 

Hello Freesurfer devs,

 

I ran the hippocampal and amygdala subfields command in my sample and I get the following error in several subjects:

 

Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)

 

MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de 2018, 21:37:33 CEST

 

 

 

What would be the reason?

 

 

Thanks in advance,

 

 

Best wishes,


--

Miguel Ángel Rivas Fernández

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