External Email - Use Caution Hi Eugenio,
It was happened in only in 17 subjects (sample size is 295). I repeated the process several times and I got always the same error. Thank you very much for your help!. Cheers, El dom., 16 sept. 2018 a las 19:14, Iglesias Gonzalez, Eugenio (< e.igles...@ucl.ac.uk>) escribió: > 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>) 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> on behalf of Miguel > Ángel Rivas Fernández <miguelrivasf...@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 > <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 > 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* > _______________________________________________ > Freesurfer mailing list > 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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