External Email - Use Caution 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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasf...@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 External Email - Use Caution Hi Eugenio, I have downloaded the most recent dev version ( freesurfer-darwin-OSX-ElCapitan-dev.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/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<http://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.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>) escribió: External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández <miguelrivasf...@gmail.com<mailto:miguelrivasf...@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, 13 September 2018 at 21:12 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<http://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. -- Miguel Ángel Rivas Fernández
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