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-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.gzftp://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.eshttp://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.ukmailto: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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 13 September 2018 at 21:12 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.eshttp://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.edumailto: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

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 (< miguelrivasfdez@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.iglesias@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-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

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

*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

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*