Hi all,
I believe the website warns for high demands of memory, claiming it may take up to 10G for this processing step. However, when I run this on cluster the memory demands go up to 30G. This is still for one subject using one scan. Is this to be expected, has something changed in the processing pipeline?
Eventually I want to run the longitudinal version, should I expect an increase in memory demands?
Running the parahippocampal subfields on our cluster using: recon-all -s $subject -hippocampal-subfields-T1
Version: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Kind regards,
Ferdi
Hi Ferdi, Sorry for the late response. Is this a standard resolution (1mm) T1? I’m very surprised; it’s never required more than 14GB on our data. 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 16 Mar 2017, at 14:02, Ferdi van de Kamp <ferdivdkamp@gmail.commailto:ferdivdkamp@gmail.com> wrote:
Hi all,
I believe the website warns for high demands of memory, claiming it may take up to 10G for this processing step. However, when I run this on cluster the memory demands go up to 30G. This is still for one subject using one scan. Is this to be expected, has something changed in the processing pipeline?
Eventually I want to run the longitudinal version, should I expect an increase in memory demands?
Running the parahippocampal subfields on our cluster using: recon-all -s $subject -hippocampal-subfields-T1
Version: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Kind regards,
Ferdi _______________________________________________ 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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Hi Eugenio,
I've been trying figure out what is going on and part of the problem seems to be a buggy scheduler, which cannot be remedied at the moment. E.g. 64G maxvmem is reached in one subject within 12 seconds (when running a batch of over 100 participants). Running it again later (in a very small batch of 3 subjects) results in a succesful processing at maxvmem of 19G..
The scans we use have these dimensions, are they in any way problematic?
data_type INT16 dim1 256 dim2 256 dim3 140 dim4 1 datatype 4 pixdim1 0.8750000000 pixdim2 0.8750000000 pixdim3 1.2000000477 pixdim4 0.0000000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
Cheers,
Ferdi
Ha, that’s funny. The dimensions seem perfectly fine to me …
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 30 Mar 2017, at 09:16, Ferdi van de Kamp <ferdivdkamp@gmail.commailto:ferdivdkamp@gmail.com> wrote:
Hi Eugenio,
I've been trying figure out what is going on and part of the problem seems to be a buggy scheduler, which cannot be remedied at the moment. E.g. 64G maxvmem is reached in one subject within 12 seconds (when running a batch of over 100 participants). Running it again later (in a very small batch of 3 subjects) results in a succesful processing at maxvmem of 19G..
The scans we use have these dimensions, are they in any way problematic?
data_type INT16 dim1 256 dim2 256 dim3 140 dim4 1 datatype 4 pixdim1 0.8750000000 pixdim2 0.8750000000 pixdim3 1.2000000477 pixdim4 0.0000000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
Cheers,
Ferdi _______________________________________________ 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.
freesurfer@nmr.mgh.harvard.edu
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Ferdi van de Kamp -
Iglesias Gonzalez, Eugenio