OK, thank you. I've read both these papers but it's been a while - do you mind if I ask where specifically you see that this misatribution is problematic for events in mixed designs rather than events in an event only design?
I would be interested in using the FIR function. I'm assuming that using a fixed function is not problematic for modeling the blocks though, right? Unfortunately the fsl wiki appears to be down now, so I can't see how to implement FLOBS. for FIR, I'm assuming I can just modify the fsf files before feat_model. Thank you, Michael On Thu, Sep 22, 2016 at 3:35 PM, Burgess, Gregory <gburg...@wustl.edu> wrote: > If you’re referring to what is sometimes called a “state-item” design (cf. > http://www.nil.wustl.edu/labs/schlaggar/Publications_files/ > MIxedBlockPaper_Final.pdf), you should not use a canonical / assumed > response shape. That’s because the variance that is not captured by your > assumed HRF can be misattributed to your state / sustained regressor. > > For these designs, your event-related effects should be modeled with a > basis set that will capture varying response shapes (e.g., FIR or FLOBS) to > ensure that you do not misattribute poorly-modeled activation to the > sustained regressor. I don’t know much about the inverse logit basis set, > but you might consider looking at it too (Lindquist et al. 2009). An > advantage of the FIR basis set is that you can easily look for interactions > with “time” to test if the response shape varies between regions or > individuals. > > Lindquist, M. A., Meng Loh, J., Atlas, L. Y., & Wager, T. D. (2009). > Modeling the hemodynamic response function in fMRI: efficiency, bias and > mis-modeling. NeuroImage, 45(1 Suppl), S187–98. http://doi.org/10.1016/j. > neuroimage.2008.10.065 > > --Greg > > ____________________________________________________________________ > Greg Burgess, Ph.D. > Staff Scientist, Human Connectome Project > Washington University School of Medicine > Department of Psychiatry > Phone: 314-362-7864 > Email: gburg...@wustl.edu > > > On Sep 22, 2016, at 2:05 PM, Michael Dreyfuss <mdreyfus...@gmail.com> > wrote: > > > > Thank you both. > > > > This is for our task which is actually a mixed design. I'm not too > concerned about the blocks because like you say the main goal is estimating > amplitude there. For the jittered events, however, I would want more > flexibility in the basis function because like you said the HRF could have > quite different shapes in different regions and different individuals. > Regardless, the activation patterns I'm seeing seem reasonable. I'm just > wondering if the double gamma is also better fitted to visual cortex and so > activation there is more detectable than in other regions, and if so maybe > activity in other regions would be better detected using a more flexible > basis function like FLOBS of FIR. I think your explanation about proximity > to the head coil may be a big part of that too, though, so I'm reluctant to > assume there is a problem with using double gamma (and there is a cost to > estimating the basis function everywhere too). > > > > I will continue to look into these other options... > > > > Thanks again, > > Michael > > > > On Thu, Sep 22, 2016 at 2:31 PM, Burgess, Gregory < > burge...@psychiatry.wustl.edu> wrote: > > Hi Michael, > > > > A few things: > > 1) Matt’s point about the increased activation estimates in visual > cortex is a good one. There is increased signal in occipital cortex in > functional connectivity analyses that do not assume a response shape. In > part, this may result from the back of the head being closer to the head > coil than other brain regions (because participants are laying down). > > 2) To the best of my knowledge, the HCP consortium has not ventured to > recommend a single, ideal HRF for use in task fMRI analysis. In fact, I’d > wager that most people in the consortium expect the hemodynamic response to > vary across brain regions and across people in such a way that there is no > single ideal canonical HRF. > > 3) We chose the double-gamma during very early analysis of HCP pilot > data. Using 2.5s TR data, the default double-gamma showed zstat maps with > slightly higher statistical significance at the group-level than the > default gamma HRF (in Feat). The double-gamma also seemed to be used more > widely in the literature, in part due to the commonly observed undershoot > at the end of the hemodynamic response (see Glover, 1999). We made this > choice in piloting, and stayed with it for analysis of the Phase II HCP. We > did not re-evaluate HRFs in the fast TR HCP data. > > 4) In HCP tfMRI, we utilized blocked designs. Blocked designs are good > for detecting the response, but are not good for estimating the shape of > the response function. It may follow that differences between canonical > HRFs will matter less for blocked designs, but I don’t know if anyone has > looked at that systematically. > > 5) If you’re referring to analysis of your own data using an > event-related design, your best bet will likely be using a basis set. FSL > has FLOBS, folks at Wash U tend to use FIR basis sets, but there are others > out there as well. There are quite a few papers out there to help you > choose between those basis sets. However, I’m not sure it would make much > sense in the context of a blocked design. > > > > Hope this all helps! > > --Greg > > > > ____________________________________________________________________ > > Greg Burgess, Ph.D. > > Staff Scientist, Human Connectome Project > > Washington University School of Medicine > > Department of Psychiatry > > Phone: 314-362-7864 > > Email: gburg...@wustl.edu > > > > > On Sep 22, 2016, at 12:25 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > > > > > > BOLD fluctuations are generally stronger on the occipital cortex > > > (independent of the chosen HRF). See for example the attached > functional > > > CNR map (BOLDVariance / UnstructuredNoiseVariance). > > > > > > Peace, > > > > > > Matt. > > > > > > On 9/21/16, 7:29 PM, "hcp-users-boun...@humanconnectome.org on behalf > of > > > Michael Dreyfuss" <hcp-users-boun...@humanconnectome.org on behalf of > > > mdreyfus...@gmail.com> wrote: > > > > > >> Hello, > > >> > > >> What kind of basis function are you recommending for tfMRI data?I have > > >> been using double-gamma HRF but I notice that the signal is always > > >> strongest in occipital cortex, so I was wondering if this is not > optimal > > >> for other regions. If so, do you have a more customized recommendation > > >> that would better fit HRF functions in other parts of the brain to > detect > > >> signal there? > > >> > > >> Thank you, > > >> Michael > > >> _______________________________________________ > > >> 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 > > > <BOLDCNR.png> > > > > > > ________________________________ > > 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. 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