Just a few comments: 1) I agree with Maarten that FIX-denoising is effectively removing WM and CSF components from the FIX timeseries data. My understanding is that Matt Glasser has evaluated the incremental benefit for regressing the (average) WM and CSF timeseries and concluded that there is no additional benefit after FIX. I don’t believe that anyone has tested whether additional WM and CSF components (such as implemented in CompCor) can remove noise variance above and beyond FIX, though, in theory, FIX should capture those as well.
2) Some analyses that I have conducted suggest that FIX denoising may leave behind some proportion of physiological noise, especially that which is more globally-distributed across gray matter. I am hoping to investigate whether physiological regressors can remove that additional proportion. 3) It is probably important to regress physiological regressors, motion regressors, and FIX noise regressors simultaneously from the timeseries. Otherwise, the fit of some regressors to the timeseries will be worsened by removing the other regressors from the timeseries. It might work to regress motion and noise ICs from the physio regressors, and then regress physio from the FIX timeseries, but I am not certain that it will (e.g., for RETROICOR-type regressors). 4) If you decide to investigate physiological regressors, please use those release in the 900 subject packages, because the physiological measures in the 500 subject release had a timing bug. There will be additional information about the updated physiological measures coming in the near future. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Neuroscience Phone: 314-362-7864 Email: [email protected] > On Dec 9, 2015, at 4:40 PM, Maarten Mennes <[email protected]> wrote: > > One could also argue that WM and CSF regression is not needed anymore if the > FIX denoising worked as intended... Given that FIX will look for components > that correlate with WM and CSF signal these signals are already regressed out > if components were properly identified. The same is true for the > physiological data. > > Note that this is different from a tool like ICA-AROMA which is not trained > to identify WM/CSF/physiological components, in this case extra nuisance > regression might effectively come in handy. But I don't see this need in > FIX-denoised data. > > Or am I missing something obvious? > > Cheers, > Maarten > > > On Wed, Dec 9, 2015 at 11:10 PM, Harms, Michael <[email protected]> wrote: > > See inline below. > > -- > 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 > St. Louis, MO 63110 Email: [email protected] > > From: Joelle Zimmermann <[email protected]> > Date: Wednesday, December 9, 2015 3:08 PM > To: "Harms, Michael" <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] FIX-denoised > > Hi Michael, > > Thanks for your help. I have a few more questions below.. > > Has an average timeseries for WM (and CSF) signal been already computed by > HCP? > Perhaps this is the "rfMRI_REST1_LR_WM.txt" and the "rfMRI_REST1_LR_CSF.txt" > in the FIX extended package? > Yes, you could use those. See the scripts in the RestingStateStats folder in > github if you want to know the details of how exactly those were derived. > But see next for some downstream files that you could use instead that would > save you a lot of methodological preparation. > > Is there a recommended way of regressing these out? > Take a look at the RestingStateStats/RestingStateStats.m code. In > particular, if starting from the "MPP" WM and CSF time courses (i.e., from > the non-cleaned data) you need to apply the same HP filter, and regress out > the motion parameters and the FIX-identified noise components, so that you > don’t re-introduce noise related to those operations into the cleaned data. > And if you were to regress out WM and CSF sequentially, then you need to do > something similar to account for the order there as well. It gets a bit > complicated. :) > > Fortunately, looking at the RestingStateStats.m script, there should be files > "*_Cleaned{WM,CSF}tc.txt" that have already done all that for you. In which > case, all you need to do is use those simultaneously in a regression to > remove the noise space spanned by those two already supplied > "*_Cleaned{WM,CSF}tc.txt" files from the hp2000_clean.nii.gz volume data or > hp2000_clean.dtseries.nii CIFTI data. (See e.g., Lines 330-334 in > RestingStateStats.m for what I mean by using them in a "simultaneous" > regression). > > I think I have that right, but Matt wrote that particular bit of code, so > hopefully he will correct if I've misstated anything. > > Related to my previous question: Has physiological data > (“rfMRI_REST1_LR_Physio_log”) already been regressed from the FIX denoised > data? > I cannot actually find a rfMRI Physio log file in the FIX-ed dataset, I can > only find this Physio log file in the minimally preprocessed dataset. I > suppose I can use that one? But I'd assume there should be one in the FIX-ed > dataset folder as well... > We haven't yet extended the RestingStateStats.m code to incorporate > regressors derived from the physio files, which is why the physio time series > isn't also part of the FIX-extended packages. If you want to try regressing > out physio as well, again make sure that you first regress out of any physio > regressors all the preceding filtering/regression steps, so that you don't > re-introduce any previously removed noise from the cleaned data. > > > Thanks, > Joelle > > On Wed, Dec 9, 2015 at 2:43 PM, Harms, Michael <[email protected]> wrote: > > Hi, > See inline below. > > -- > 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 > St. Louis, MO 63110 Email: [email protected] > > From: Joelle Zimmermann <[email protected]> > Date: Wednesday, December 9, 2015 1:26 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] FIX-denoised > > Hi everyone, > > I'm interested in using the FIX-denoised data, and am currently looking at > the extended package, as I'm interested in the volumetric data. > > I'm wondering whether the motion parameters have already been regressed out > from the FIX denoised rfMRI_REST1_LR_hp2000_clean.nii.gz? > YES > > I'm assuming yes, that the FIX denoised actually already deals with this by > separating the motion-related noise into a component and filtering that out > of the signal? I assume so based on the following snippet from the manual > describing FIX-ed data: > "As part of this cleanup, we also used 24 confound timeseries derived from > the motion estimation (the 6 rigid-body parameter timeseries, their > backwards-looking temporal derivatives, plus all 12 resulting regressors > squared — Satterthwaite et al., 2013). The motion parameters have the > temporal highpass filtering applied to them and are then regressed out of the > data aggressively, as they are not expected to contain variance of interest." > Am I correct? > YES > > Has white matter and/or cerebrospinal fluid been regressed already from the > FIX denoised fMRI timeseries? > NO > > Has physiological data (“rfMRI_REST1_LR_Physio_log”) already been regressed > from the FIX denoised data? > NO > > Any pointers would be much appreciated. > > Thanks, > Joelle > > > > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > -- > Maarten Mennes, Ph.D. > Senior Researcher > Donders Institute for Brain, Cognition and Behaviour > Radboud University Nijmegen > Nijmegen > The Netherlands > > Google Scholar Author Link > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
