External Email - Use Caution Hi Eugenio,
Did you have chance to review the error that I have reported some days ago when I ran the hippocampal and amygdala command? It was happened only in 17 subjects (sample size 295). I rerun the HippocampalSubfieldsandAmygdalaNuclei command and I got the same error: *Fitting mesh to image data mask took 683.6633 secondsTransforming pointsTransforming pointsWrote image to file image.mgzINFO: 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.mgzvolume 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.niiConstructing 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.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)MATLAB:subsassignnumelmismatchDarwin 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_64T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35 CESTFor 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 dom., 16 sept. 2018 a las 19:20, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > 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* > -- *Miguel Ángel Rivas Fernández*
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
