Dear experts, I am running running hippocampal subfield segmentation using the most recent version of the FSv6.0 on LinuxMint 17.3 Rosa.
For some (~ 25%, but not all) participants I did not get the subfields. I have later realized that although segmentation finished with out errors, I got the following message in the end:
Error using kvlGEMSMatlab std: :bad_alloc
Error in kvlRasterizeAtlasMesh (line 11)
Error in segmentSubjectT1_autoEstimateAlveusML (line 628).
I have read that I need to check whether the T1resampled.mgz actually exists in the temporary directory of the subject. I have checked and this file is indeed there: SBJ/tmp/hippoSF_T1_v10_right/T1resampled.mgz.
Please, let me know if this is a known problem and if there is anything I can do to correct it?
Thank you very much in advance,
Artyom
Dear Artyom, You’re probably running out of RAM memory in those few cases. How much RAM do you have? Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 19 May 2017, at 15:31, Artyom Zinchenko <Artyom.Zinchenko@psy.lmu.demailto:Artyom.Zinchenko@psy.lmu.de> wrote:
Dear experts,
I am running running hippocampal subfield segmentation using the most recent version of the FSv6.0 on LinuxMint 17.3 Rosa.
For some (~ 25%, but not all) participants I did not get the subfields. I have later realized that although segmentation finished with out errors, I got the following message in the end:
Error using kvlGEMSMatlab std: :bad_alloc
Error in kvlRasterizeAtlasMesh (line 11)
Error in segmentSubjectT1_autoEstimateAlveusML (line 628).
I have read that I need to check whether the T1resampled.mgz actually exists in the temporary directory of the subject. I have checked and this file is indeed there: SBJ/tmp/hippoSF_T1_v10_right/T1resampled.mgz.
Please, let me know if this is a known problem and if there is anything I can do to correct it?
Thank you very much in advance,
Artyom
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Dear Eugenio,
Thank you very much for the prompt reply, it seems like RAM was the key, it works now. Thank you once again.
Artyom
"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 19.05.17 16.48
Uhr >>> Dear Artyom, You’re probably running out of RAM memory in those few cases. How much RAM do you have? Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 19 May 2017, at 15:31, Artyom Zinchenko Artyom.Zinchenko@psy.lmu.de wrote:
Dear experts, I am running running hippocampal subfield segmentation using the most recent version of the FSv6.0 on LinuxMint 17.3 Rosa.
For some (~ 25%, but not all) participants I did not get the subfields. I have later realized that although segmentation finished with out errors, I got the following message in the end:
Error using kvlGEMSMatlab std: :bad_alloc
Error in kvlRasterizeAtlasMesh (line 11)
Error in segmentSubjectT1_autoEstimateAlveusML (line 628).
I have read that I need to check whether the T1resampled.mgz actually exists in the temporary directory of the subject. I have checked and this file is indeed there: SBJ/tmp/hippoSF_T1_v10_right/T1resampled.mgz.
Please, let me know if this is a known problem and if there is anything I can do to correct it?
Thank you very much in advance,
Artyom
_______________________________________________ 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.
freesurfer@nmr.mgh.harvard.edu
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Artyom Zinchenko -
Iglesias Gonzalez, Eugenio