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Wow sorry about this. I have to carefully check whether it’s a different / related bug, or if the fix only made it to the Linux version. Is it happening for all subjects, or only some?
I’m traveling / on vacation these days but will take a look as soon as I can.
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
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: Sunday, 16 September 2018 at 15:52
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
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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
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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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.