[Freesurfer] Parallelizing on a different kind of cluster
Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo ___ 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.
Re: [Freesurfer] Parallelizing on a different kind of cluster
Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo ___ 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.
Re: [Freesurfer] Parallelizing on a different kind of cluster
Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parallelizing on a different kind of cluster
Everything that's in bedpostx is also in bedpostx_seychelles. I've just added to it. But if you want to run bedpostx directly on the command line instead of going through trac-all -bedp, you can do that, too. On Tue, 12 Feb 2013, Susie Kuo wrote: Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parallelizing on a different kind of cluster
I see. So I will discriminate between what bedpostx requires from the more inclusive bedpostx_seychelles script. Thank you for your help. I sincerely appreciate it. Best, Susie Kuo On Tue, Feb 12, 2013 at 1:56 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Everything that's in bedpostx is also in bedpostx_seychelles. I've just added to it. But if you want to run bedpostx directly on the command line instead of going through trac-all -bedp, you can do that, too. On Tue, 12 Feb 2013, Susie Kuo wrote: Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo 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/**compliancelinehttp://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 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.
