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Re: ROI based resting state analysis

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Fri, 14 Aug 2009 15:46:03 +0100

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 ```Thanks Christian. I did not know if there was a stand alone GS decomposition routine in FSL so I instead used matlab's orth function instead to find the orthonormal basis of my signal and nuisance time series. It of course produced a completely different orthonormal basis than GS. It uses singular value decomposition. I get an interesting set of results with this but have no idea if they have any sort of meaning. I know this isn't an FSL question per se, but do you have any idea if there is a statistical interpretation to the time series produced by the SVD algorithm? Thanks again, Tal. On Thu, 13 Aug 2009 21:34:24 +0100, Christian F. Beckmann <[log in to unmask]> wrote: >Hi > >It's identical, see the wiki description of GS, i.e. when using GS on >two vectors v1 and v2, the new vectors are v1 and v2-proj(v1,v2) > >That is, you create the second vector by removing any correlation with >the first. >And yes, you don;t want to fully orthogonalise everything with >everythinge else - in fact if you simply add the nuisance regressors >then things will already be taken of. >hth >Christian > > > > > >On 13 Aug 2009, at 17:22, Tal Herbsman wrote: > >> A couple of of further questions, please forgive the ignorance/ >> confusion, it's been a while >> since linear algebra: >> >> My understanding is that the GS de gives an orthonormal basis for >> the function space. It's >> not intuitively clear to me that this the same thing as covarying >> nuisance signals out of a >> time series. >> >> My application is not VBM whole brain correlation but rather a set >> of n ROI based >> timeseries cross-correlated with each other. Would GS decomposition >> of [ROI1 ... ROIn >> Nuisance1 ... NuisanceM] not ensure that I get no cross correlation >> (as opposed to cross >> correlating each ROI decomposed with only the nuisance variables? >> >> Tal. >> >> On Thu, 13 Aug 2009 10:25:22 +0100, Christian F. Beckmann >> <[log in to unmask]> wrote: >> >>> Hi >>> >>> Yes, the description of the method is very inclusive. Only issue I >>> have is that I'd advice using the Eigen-timeseries rather than the >>> mean timeseries within the ROIs for further analysis >>> hth >>> Christian >>> >>> >>> >>> On 13 Aug 2009, at 04:02, Xue, Feng wrote: >>> >>>> Here is an good example for ROI time series data correlation in RS- >>>> fMRI: >>>> >>>> "Mapping the functional connectivity of anterior cingulate cortex" >>>> by Daniel S. Marguliesa, A.M. Clare Kellya, Lucina Q. Uddina, Bharat >>>> B. Biswalb, F. Xavier Castellanosa, c, , and Michael P. Milham >>>> NeuroImage >>>> Volume 37, Issue 2, 15 August 2007, Pages 579-588 >>>> >>>> On Thu, Aug 13, 2009 at 12:19 AM, Tal Herbsman<[log in to unmask]> >>>> wrote: >>>>> Dear FSL users, I would appreciate some advice on this: I am >>>>> interested in doing >>>>> correlation analysis on time series data extracted w/ fslmeants of >>>>> various anatomical >>>>> ROIs from FEAT preprocessed fMRI data. I have a set of nuisance >>>>> time series (CSF, WM >>>>> and whole brain global drifts). What would be the correct way of >>>>> regressing these >>>>> nuisance covariates out of my time series? I can think of two ways >>>>> but am not sure which >>>>> (if any) is correct, nor how to implement them: >>>>> >>>>> 1. orthogonalize the ROI time series with respect to global drift >>>>> time series. Is the FSL >>>>> orthogonalization available as a separate command line program? >>>>> >>>>> 2. use GLM to figure out PEs for nuisance regressors and subtract >>>>> from signal. Not sure >>>>> how to go about doing this. >>>>> >>>>> Any ideas? >>>>> >>>>> Tal. >>>>> >>>>> >>>>> Tal Herbsman, MD >>>>> >>>>> Assistant Professor >>>>> Department of Psychiatry >>>>> University of Wisconsin School of Medicine and Public Health >>>>> 6001 Research Park Blvd. >>>>> Madison, WI 53719-1176 >>>>> >>>>> Office: (608) 263-6100 >>>>> Fax: (608) 263-0265 >>>>> [log in to unmask] >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Best Regards >>>> >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>> >>> _______________________________________________ >>> Christian F. Beckmann, DPhil >>> Senior Lecturer, Clinical Neuroscience Department >>> Division of Neuroscience and Mental Health >>> Imperial College London, Hammersmith Campus >>> Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK >>> Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 >>> Email: [log in to unmask] >>> http://www.imperial.ac.uk/medicine/people/c.beckmann/ >>> >>> Senior Research Fellow, FMRIB Centre >>> University of Oxford >>> JR Hospital - Oxford OX3 9DU >>> Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717 >>> Email: [log in to unmask] >>> http://www.fmrib.ox.ac.uk/~beckmann > >_______________________________________________ >Christian F. Beckmann, DPhil >Senior Lecturer, Clinical Neuroscience Department >Division of Neuroscience and Mental Health >Imperial College London, Hammersmith Campus >Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK >Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 >Email: [log in to unmask] >http://www.imperial.ac.uk/medicine/people/c.beckmann/ > >Senior Research Fellow, FMRIB Centre >University of Oxford >JR Hospital - Oxford OX3 9DU >Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717 >Email: [log in to unmask] >http://www.fmrib.ox.ac.uk/~beckmann ```