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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
From: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Date: Wednesday, 10 October 2018 at 09:39
To: "Iglesias Gonzalez, Eugenio" <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.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:
- Delete new version with: rm –rf $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app
- 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
From: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Date: Wednesday, 3 October 2018 at 18:32
To: "Iglesias Gonzalez, Eugenio" <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.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
From: Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Date: Wednesday, 3 October 2018 at 18:07
To: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Cc: "ahoopes@mgh.harvard.edu" <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.com>) escribió:
Thanks a lot!
Miguel,
El lun., 1 oct. 2018 a las 8:39, Iglesias Gonzalez, Eugenio (<e.iglesias@ucl.ac.uk>) escribió:
Thanks a lot!
Sent from my phone, please excuse brevity and typos
From: Hoopes, Andrew <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.uk>
Date: Sunday, September 30, 2018 at 10:47 AM
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>, Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Subject: FW: [Freesurfer] Hippocampal-Amygdala subfields error
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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
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, 26 September 2018 at 00:09
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error
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 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 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.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:
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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
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 ) 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 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:
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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 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
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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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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
--Miguel Ángel Rivas Fernández
--Miguel Ángel Rivas Fernández
--Miguel Ángel Rivas Fernández
--
Miguel Ángel Rivas Fernández