Thanks Matt That's correct that the --migp option (see a recent post from me to the FSL list about this new option) inside melodic is still single-threaded.
However the journal paper (linked below by Matt) includes simple matlab code for doing MIGP and that can easily be parallelised as well as run multi-threaded. The output can then be fed into melodic ICA. Neither MIGP approach requires huge RAM - that's the point - 32GB should be enough. Cheers. > On 30 Jan 2015, at 03:32, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > > http://www.sciencedirect.com/science/article/pii/S105381191400634X > <http://www.sciencedirect.com/science/article/pii/S105381191400634X> > > We’re working on some improvements for it when used for functional > connectivity (i.e. all to all correlations), but it works fine as is for ICA. > > > Peace, > > Matt. > > From: Micah Chambers <micahc...@gmail.com <mailto:micahc...@gmail.com>> > Date: Thursday, January 29, 2015 at 9:27 PM > To: Matt Glasser <glass...@wusm.wustl.edu <mailto:glass...@wusm.wustl.edu>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects > > Thanks Matthew, I'll check out the latest version of FSL. Is there a paper > the discusses the MIGP method? > > On Thu, Jan 29, 2015 at 7:24 PM, Micah Chambers <micahc...@gmail.com > <mailto:micahc...@gmail.com>> wrote: >> Well the resting state data provided through the HCP around 1GB each so I'm >> guessing the memory requirement is a good bit more than 8GB now, unless the >> PCA is performed per subject. Has anyone done Group ICA on datasets this >> size? >> >> -Micah >> >> On Thu, Jan 29, 2015 at 6:40 PM, Glasser, Matthew <glass...@wusm.wustl.edu >> <mailto:glass...@wusm.wustl.edu>> wrote: >>> If you update to the latest version of FSL the MIGP algorithm may be in >>> there and is designed to help with this. The main limitation with melodic >>> has been that it was single threaded. I don’t know if that has been >>> addressed yet. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Micah Chambers <micahc...@gmail.com <mailto:micahc...@gmail.com>> >>> Date: Thursday, January 29, 2015 at 8:07 PM >>> To: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" >>> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> >>> Subject: [HCP-Users] Group ICA with Melodic on 20 or more subjects >>> >>> Has anyone on the run group-wise analysis on the HCP resting state data, >>> and if so what tools did you use? I am having memory issues when running >>> more than 10 subjects and I was wondering if anyone has a way of getting >>> around the large memory requirements when concatenating in time. >>> >>> Thanks! >>> >>> -Micah >>> >>> -- >>> Micah Chambers, M.S. >>> Ahmanson-Lovelace Brain Mapping Center >>> University of California Los Angeles >>> 635 Charles E. Young Drive SW, Suite 225 >>> Los Angeles, CA 90095-7334 >>> 310-206-2101 <tel:310-206-2101> (Office) >>> 310-206-5518 <tel:310-206-5518> (Fax) >>> 703-307-7692 <tel:703-307-7692> (Cell) >>> email: mica...@ucla.edu <mailto:mica...@ucla.edu> >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >>> >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >> >> >> >> -- >> Micah Chambers, M.S. >> Ahmanson-Lovelace Brain Mapping Center >> University of California Los Angeles >> 635 Charles E. Young Drive SW, Suite 225 >> Los Angeles, CA 90095-7334 >> 310-206-2101 <tel:310-206-2101> (Office) >> 310-206-5518 <tel:310-206-5518> (Fax) >> 703-307-7692 <tel:703-307-7692> (Cell) >> email: mica...@ucla.edu <mailto:mica...@ucla.edu> >> >> > > > > -- > Micah Chambers, M.S. > Ahmanson-Lovelace Brain Mapping Center > University of California Los Angeles > 635 Charles E. Young Drive SW, Suite 225 > Los Angeles, CA 90095-7334 > 310-206-2101 (Office) > 310-206-5518 (Fax) > 703-307-7692 (Cell) > email: mica...@ucla.edu <mailto:mica...@ucla.edu> > > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
