Hi, Matt and Stephen: Thanks for your responses. So I will try below three options to see which one is better.
1. ICA+FIX on each 5 min run separately 2. Concatenate each pair of scans from each session and then ICA+FIX on each session 3. Use multi-run ICA+FIX to combine across runs I have another simple question. In the paper published in NeuroImage (Smith et al., 2013, rfMRI in the HCP), the Figure 9 shows functional connectivity in the default mode network; one is from 15 min run from single subject, another one is from 4*15 min runs from single subject, and the other one is from all subjects concatenated. How did you process the data to present those figures (second and third one)? The third one should be processed with group ICA, right? What about the second one? This is processed with method 3 on above list? Thanks. Sang-Young > On Oct 6, 2017, at 5:40 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > > There is a beta version of a multi-run ICA+FIX pipeline available in the HCP > Pipeline’s repository. For 5 minute runs, I would expect combining across > runs to be best. We haven’t tested combining across sessions yet, so you > would have to check that that was working okay if you wanted to try that. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Stephen Smith > <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> > Date: Friday, October 6, 2017 at 1:49 AM > To: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding > directions > > Hi - I think your main two choices are whether to run FIX on each 5min run > separately, or to preprocess and concatenate each pair of scans from each > session and run FIX for each of the 4 paired datasets. You could try FIX > both ways on a few subjects and decide which is working better. > > Cheers. > > > >> On 5 Oct 2017, at 22:53, Sang-Young Kim <sykim...@gmail.com >> <mailto:sykim...@gmail.com>> wrote: >> >> Dear Experts: >> >> We have acquired rfMRI dataset with A-P and P-A phase encoding direction and >> the data was acquired in eight 5-minute runs split across four imaging >> sessions. We have processed the data using HCP pipelines (e.g., >> PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface and >> ICA+FIX). So we have results for each run of rfMRI data. >> >> I’m just curious about what is recommended way to combine each run of data >> (e.g., rfMRI_REST1_AP, rfMRI_REST1_PA, …, rfMRI_REST4_AP, rfMRI_REST4_PA). >> >> Can we just temporally concatenate each run of data before running ICA+FIX? >> Or can we do group ICA using each data processed with ICA+FIX? >> What is the optimal way to do combining analysis across each run? >> >> Any insights would be greatly appreciated. >> >> Thanks. >> >> Sang-Young Kim >> *********************************************************** >> Postdoctoral Research Fellow >> Department of Radiology at University of Pittsburgh >> email: sykim...@gmail.com <mailto:sykim...@gmail.com> >> *********************************************************** >> >> >> _______________________________________________ >> 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> > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > st...@fmrib.ox.ac.uk <mailto: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 <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
