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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
