Re: [Freesurfer] any way to parallelize Tracula?
Hi all, Good news. I was able to submit the job to our cluster using the -s flag of the trac-all command. Once I did that, I just wrote a loop to go through my subjects and was good to go. --Matt -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 1:02 PM To: Susan Kuo Cc: Hoptman, Matthew; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] any way to parallelize Tracula? Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _ _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using
Re: [Freesurfer] any way to parallelize Tracula?
Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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] any way to parallelize Tracula?
Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**__** __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] any way to parallelize Tracula?
Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _ _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ 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] any way to parallelize Tracula?
Hi Anastasia, I am operating on 5.1... I'm glad to know that there is such a huge difference in versions; and that there's so much gain in upgrading. I will look at the fsl_sub_mgh script, and I'll post back what I figure out (if anything), if other people are interested. Otherwise, it's vox clamantis en deserto... Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 1:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**__** _ _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
