Dear Michael, Please let me know if my understanding is correct.
I am trying to get my hands on the input matrix G (Group time series data) in Figure 2 I took Matt's reply to mean that Steve Smith generated G, and Matt's ICA+FIX would be downstream from that (i.e. not G). If that is not correct, are you saying ICA+FIX data is matrix G? (of course taking each subject and concatenating them row-wise) My understanding is FSLNets would take G^T G as input Thank you, Sang On Fri, May 12, 2017 at 2:27 PM Harms, Michael <mha...@wustl.edu> wrote: > > No, ICA+FIX is data cleanup that is applied to the minimally preprocessed > (MPP) data. > > I suggest you start here > https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLNets > and in particular the file “nets_examples.m” > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Sang-Yun Oh < > san...@gmail.com> > Date: Friday, May 12, 2017 at 4:10 PM > To: "Glasser, Matthew" <glass...@wustl.edu>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, Stephen > Smith <st...@fmrib.ox.ac.uk> > Subject: Re: [HCP-Users] Replicating "Resting-state fMRI in the Human > Connectome Project" > > Dear Matt, > > Thank you for your quick response. > > Would that mean matrix G is derived from minimally preprocessed data? > > If so, how can I reconstruct G from minimally preprocessed data? > > Thank you, > Sang > > On Fri, May 12, 2017 at 1:55 PM Glasser, Matthew <glass...@wustl.edu> > wrote: > >> Steve Smith would have generated that matrix. I would have been after >> running ICA+FIX, which would remove linear trends, 24 movement regressors >> and ICA noise component timeseries. >> >> The matrix would have been made with FSLNets. >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Sang-Yun Oh < >> san...@gmail.com> >> Date: Saturday, May 13, 2017 at 5:38 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Replicating "Resting-state fMRI in the Human >> Connectome Project" >> >> Dear HCP users, >> >> I am new to this area and I would like to do a replication exercise to >> learn more about HCP dataset and neuroscience tools. >> >> What would be the simplest way to get my hands on matrix G (Figure 2) in >> this paper? https://doi.org/10.1016/j.neuroimage.2013.05.039 I would >> imagine G is after regressing out any motion and white matter signals (is >> this true?) >> >> I tried to read the supplemental material; however, it was very complex >> and way over my head. >> >> Is there a script available for computing G from HCP released data that a >> newbie like me can use? >> >> I would appreciate any guidance >> >> Best, >> Sang >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> 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. >> > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > 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. > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
