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Dear Miguel Angel, Ideally, one would always run all the subjects on the same platform. If this is completely impractical due to computational limitations, then it is very important to: - spread the groups across platforms, e.g., avoid running all controls on one platform, and all diseased on another, or e.g., all younger subjects on one platform, and older on another. In you don’t do this, you will never know whether detected effects are due to actual differences in brain structure, or processing platforms. AND - include the platform as a covariate in subsequent analysis. I hope this helps, /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: Wednesday, 10 October 2018 at 11:12 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fwd: Hippocampal-Amygdala subfields error
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Hi everyone,
Here a question and an answer of FreeSurfer experts that would be for interest.
- Could there be any difference in accuracy when the recon-all is executed on two Mac computers that have a different processor? that is, it is preferable to execute the recon-all of all the subjects in the same computer?. Sorry for this absurd question but I would be sure about this.
- Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine.
Best
---------- Forwarded message --------- From: Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Date: mié., 10 oct. 2018 a las 11:53 Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error To: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Cc: Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>
Hi again, MA. I totally forgot to attach the binary. The thing is that I don’t have it on my hard drive, so I need to recompile it, but our MAC server seems to be down ggggrrr Andrew: any ideas why breck is not responding? MA: sorry for the delay; we’ll definitely get to the bottom of this.
Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine.
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: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Date: Wednesday, 10 October 2018 at 09:39 To: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
Hi Eugenio,
It´s possible that you have forgotten to attach the file in this email? because I don´t find anywhere.
Another question, could there be any difference in accuracy when the recon-all is executed on two Mac computers that have a different processor? that is, it is preferable to execute the recon-all of all the subjects in the same computer?. Sorry for this absurd question but I would be sure about this.
Best,
El mié., 3 oct. 2018 a las 19:52, Iglesias Gonzalez, Eugenio (<e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk>) escribió: Allrighty, here are the instructions
(depending on the location of FREESURFER_HOME, the following commands might need to be preceded by “sudo”) 1. Save the attached file to a directory of your choice. From the terminal, cd into that directory. 2. Decompress with: tar xvf segmentSubjectT2_autoEstimateAlveusML.tar.gz 3. Move existing version of the code: mv $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old 4. Replace with new version: mv ./segmentSubjectT2_autoEstimateAlveusML.app $FREESURFER_HOME/bin/ 5. Rerun the code
If this doesn’t work, you can revert the changes with:
1. Delete new version with: rm –rf $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app 2. Restore previous version: mv $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app
If it works: there’s no need to rerun the subjects that didn’t crash.
Please let us know what happens!
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: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Date: Wednesday, 3 October 2018 at 18:32 To: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
Hi Eugenio,
I ran the command with the version freesurfer-darwin-OSX-ElCapitan (downloaded from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev) but anyway I can try with the updated executable.
If the problem solved, it is necessary to run the command with this updated executable in the subjects in which before I had no problem? I guess it would not be necessary but I would like to be sure about this.
Thanks
Cheers,
El mié., 3 oct. 2018 a las 19:17, Iglesias Gonzalez, Eugenio (<e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk>) escribió: Hi MA, I believe the FreeSurfer course is ongoing this week, which would be taking most of Andrew’s time. Our main hypothesis is that the binary with the bug fixed did not make it to the public distribution for some reason. If you want: I can send you the updated executable; you can then give it a shot, and if it solves the problem, we’ll know what the problem was. Let me know if you want to do this. Otherwise we can wait for Andrew to find time to take a look. 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: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Date: Wednesday, 3 October 2018 at 18:07 To: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Cc: "ahoopes@mgh.harvard.edumailto:ahoopes@mgh.harvard.edu" <ahoopes@mgh.harvard.edumailto:ahoopes@mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
Hi Andrew,
Did you have chance to review the error that I reported some days ago?
Thanks for your help!
Cheers,
El lun., 1 oct. 2018 a las 9:44, Miguel Ángel Rivas Fernández (<miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com>) escribió:
Thanks a lot!
Miguel,
El lun., 1 oct. 2018 a las 8:39, Iglesias Gonzalez, Eugenio (<e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk>) escribió: Thanks a lot! Sent from my phone, please excuse brevity and typos
________________________________ From: Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> Sent: Monday, October 1, 2018 4:15:12 AM To: Iglesias Gonzalez, Eugenio; Miguel Ángel Rivas Fernández Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
Sure thing, I can look into it tomorrow afternoon. Andrew
From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Date: Sunday, September 30, 2018 at 10:47 AM To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>, Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.commailto:miguelrivasfdez@gmail.com> Subject: FW: [Freesurfer] Hippocampal-Amygdala subfields error
External Email - Use Caution Hi, Andrew and MA. MA: sorry for the slow response. I’ve been on vacation (today’s my last day). Andrew: Can you please verify that the version for MAC with this bug fixed made it to the server? It’s the only explanation I can find to MA’s problems… 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: Wednesday, 26 September 2018 at 00:09 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
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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 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 dom., 16 sept. 2018 a las 19:20, Miguel Ángel Rivas Fernández (<miguelrivasfdez@gmail.commailto: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.ukmailto: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.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: Sunday, 16 September 2018 at 15:52 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
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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
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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
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-- 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
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-- Miguel Ángel Rivas Fernández
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