Hi - in general it's better to use smooth basis functions (eg as used by default in FLOBS) than "square" bases like default FIR bases. There's some literature on that but I can't quite remember now who published that - but it seems logical given that you're fitting smooth data - assuming (eg) jittering of events relative to TRs. Cheers.
> On 22 Sep 2016, at 21:44, Michael Dreyfuss <mdreyfus...@gmail.com> wrote: > > 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 > <mailto: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 > > <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 > <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 <tel:314-362-7864> > Email: gburg...@wustl.edu <mailto:gburg...@wustl.edu> > > > On Sep 22, 2016, at 2:05 PM, Michael Dreyfuss <mdreyfus...@gmail.com > > <mailto: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 <mailto: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 <tel:314-362-7864> > > Email: gburg...@wustl.edu <mailto:gburg...@wustl.edu> > > > > > On Sep 22, 2016, at 12:25 PM, Glasser, Matthew <glass...@wustl.edu > > > <mailto: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 > > > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of > > > Michael Dreyfuss" <hcp-users-boun...@humanconnectome.org > > > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of > > > mdreyfus...@gmail.com <mailto: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 <mailto:HCP-Users@humanconnectome.org> > > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > >> <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 <mailto:HCP-Users@humanconnectome.org> > > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > <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. 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 > --------------------------------------------------------------------------- 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 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
