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.iglesias@ucl.ac.uk>) escribió:
External Email - Use CautionWow 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
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.iglesias@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
*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 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
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*Miguel Ángel Rivas Fernández* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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