Thanks for your insight Matt, and I second what Chris said about the data! Don't be sad :)
On Sat, Mar 14, 2015 at 3:54 PM, Chris Filo Gorgolewski < [email protected]> wrote: > Dear Matt, > Thank you for the (super speedy) clarification. If you by any chance learn > anything more about this perplexing artefact please share it with the > mailing list. I am very curious what is causing it. > > Best, > Chris > > PS Thank you and the whole HCP team for all you hard work and all the > beautiful data you are sharing! > > On Sat, Mar 14, 2015 at 3:42 PM, Glasser, Matthew <[email protected] > > wrote: > >> Hi Chris, >> >> The task data were not cleaned with ICA+FIX or even movement parameter >> regression. As to why there is a correlation between the ventricles and a >> given contrast, that’s puzzling to me as well, but the point is that a >> strongly structured ventricle signal would get identified and removed by >> ICA+FIX (this is what it is designed to do, and it knows where the >> ventricles are in each subject). >> >> Whether or not a volume-based analysis is useful for QA, in an ideal >> world we would have already taken care of this issue for users and a >> cortical volume-based analysis is not appropriate for primary >> neuroanatomical results intended to be interpreted in relation to cortical >> functional areas or compared across studies for the reasons I stated (at >> least in my opinion). Perhaps the precipitating issue of structured noise >> in the task data needs to be revisited internally, but I know the people >> who would do any testing and analyses have many other competing priorities >> and I certainly could only provide advice for addressing that problem. >> >> Peace, >> >> Matt. >> >> From: Chris Filo Gorgolewski <[email protected]> >> Date: Saturday, March 14, 2015 at 5:31 PM >> To: Matt Glasser <[email protected]> >> Cc: vanessa sochat <[email protected]>, "[email protected]" >> <[email protected]>, Russell Poldrack <[email protected]> >> Subject: Re: [HCP-Users] De-activations in "LANGUAGE" Task Contrast Maps >> >> Hi Matt, >> Thanks for a quick reply. >> >> On Sat, Mar 14, 2015 at 3:01 PM, Glasser, Matthew < >> [email protected]> wrote: >> >>> If you don’t want ventricle activations in the task fMRI data, it >>> would be good to clean the data with something like ICA+FIX which will >>> remove spatially specific structured noise (such as whatever is causing the >>> ventricles to light up) prior to fitting the GLM. There are other stimulus >>> correlated artifacts in the task data (uncorrelated artifacts would tend to >>> get averaged out in the GLM analysis) such as strong deactivation in >>> orbitofrontal regions in the Tongue movement contrast. Use of ICA+FIX in >>> task analysis was looked at some inside the consortium, but I’m not sure if >>> there was ever a focus on seeing that stimulus correlated artifacts were >>> being removed (vs just seeing how Z-stats changed with cleanup, which they >>> don’t much since most of the variance in HCP fMRI timeseries is >>> unstructured). >>> >> Just to clarify - my understanding was that the preprocessed task data >> distributed by HCP was "cleaned" using ICA+FIX. Is that not correct? >> >> If ICA+FIX was not not used on task data do you have any ideas why >> would there be such a strong relation between the stimulus and CSF in the >> ventricles? Just to put it into perspective - the deactivation in the >> ventricles is more significant than the activation in the language areas. >> >> Also it makes me sad to see you aren’t using the CIFTI data, which are >>> substantially more accurately registered across subjects and don’t have the >>> unnecessary blurring with white matter and CSF signals (and in 3D across >>> sulci and gyri) induced by unconstrained volume-based smoothing as >>> misalignment between functional areas. The volume-based data simply don’t >>> allow you to take advantage of the high spatial resolution that the HCP >>> data were acquired with like the CIFTI data do, so you’re missing out on >>> all the cool new things you can see. >>> >> I agree using CIFTI has many advantages, but it would also make one >> completely miss the artefact Vanessa run across. Therefore I would argue, >> at least for QA purposes, that there is a justification for using volumes. >> >> Best, >> Chris >> >> >> ------------------------------ >> >> 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. >> > > -- Vanessa Villamia Sochat Stanford University (603) 321-0676 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
