Thank you Matt. This is really helpful. Any idea when the new classifier you mentioned in 1. will be available?
On Mon, Apr 22, 2019 at 8:50 PM Glasser, Matthew <glass...@wustl.edu> wrote: > I guess I haven’t been in the habit of throwing out data like this. > Things I would consider would include: > > 1. MR+FIX classification accuracy (if runs were poorly classified, > they won’t be denoised well). I’ll note that we are training an improved > MR+FIX classifier using a combination of HCP-YA resting state (single run > FIX), HCP-YA task (MR+FIX), and HCP Lifespan (MR+FIX) to address > classification issues we have observed with very large numbers of > components, subject with very large amounts of motion, and other artifacts > that were not a part of the HCP-YA original training data. > 2. Unusually small numbers of signal components (though note we found > a recent subtle bug whereby if melodic does not finish mixture modeling > components, FIX will fail to classify signal components correctly). If > there are few signal components this means that either the SNR is very bad > or the structured noise has overwhelmed the signal and mixed in too much > with the signal, making it hard to separate. > 3. DVARS Spikes above baseline (not dips below baseline) in the > cleaned timeseries suggest residual noise. I prefer DVARS derived measures > to movement tracer derived measures because they tell you something about > what is actually happening to the intensities inside the data, whereas > movement tracers may be inaccurate reflections of signal intensity > fluctuations for a variety of reasons (see Glasser et al 2018 Neuroimage: > https://www.sciencedirect.com/science/article/pii/S1053811918303963 for > examples). > > Others in the HCP used different means to identify some of the noise > components I mentioned above that weren’t being classified correctly by > regular FIX, and might be able to share their suggestions. > > Matt. > > From: Yizhou Ma <maxxx...@umn.edu> > Date: Monday, April 22, 2019 at 8:25 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement > > Thank you Matt. Do you have some suggestions for the metrics to use to > determine scan quality after ICA FIX? > > Thanks, > Cherry > > On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew <glass...@wustl.edu> > wrote: > >> I would decide after cleaning with MR ICA+FIX if you actually have to >> exclude the scans and run with them all. >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yizhou Ma < >> maxxx...@umn.edu> >> Date: Monday, April 22, 2019 at 3:47 PM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement >> >> Dear HCP experts, >> >> I am writing for a question with multi-run ICA-FIX for my dataset. I have >> 4 resting state scans (TR=0.8, length=6.5min each) and 3 task scans >> (TR=0.8, length=6min each) that I intend to run multi-run ICA-FIX on. We >> used Euclidean norm values to threshold volumes with excessive movement and >> decided that scans with more than 20% volumes with excessive movement are >> not usable. I wonder with multi-run ICA-FIX, if it would be problematic to >> include these scans. In other words, I am trying to decide if I should 1) >> run multi-run ICA-FIX on scans with less motion, therefore each subject may >> have different number of scans that are included in multi-run ICA-FIX; or >> 2) run multi-run ICA-FIX on all scans, and throw out scans with excessive >> motion afterward. >> >> Thank you very much, >> Cherry >> >> _______________________________________________ >> 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. >> > > ------------------------------ > > 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
