I would recommend ICA+FIX for HCP task fMRI data and it is unfortunate that it hasn¹t already been run (however doing this is a big enough undertaking that I haven¹t attempted it). When carefully going through the task data to create the multi-modal parcellation, there were a number of false positive findings in the task fMRI data that were very reminiscent of known structured noise in the resting state fMRI. Properly denoising the task fMRI data could cause z-statistics to go up or to go down depending on the degree to which the structured noise is correlated with the task design. What is more important is whether the change in beta maps resulting from ICA+FIX denoising shows a likely neural or likely artifactual pattern. ICA+FIX denoising of the task fMRI data might also benefit from combining across runs of the same phase encoding direction that were acquired within the same scanning session, as the task fMRI runs are shorter than the resting state fMRI runs and the more time points one has to work with, the better ICA is able to split the temporal variance into components.
Peace, Matt. On 8/2/16, 1:52 PM, "[email protected] on behalf of Burgess, Gregory" <[email protected] on behalf of [email protected]> wrote: >The FIX code includes a hcp_fix wrapper script, which you could run on >the task fMRI time series data. It should be pretty straightforward. > >However, the fact is that the 3T task data was not denoised by FIX >because the zstat maps generally _decrease_ in statistical significance >after FIX in regions where task activation is expected. This reduction >could be the result of removing task-correlated signal or removing >task-correlated noise. We have not determined that the reduced zstats are >due to noise, so we have elected to forego FIX on task fMRI for now. > >--Greg > >____________________________________________________________________ >Greg Burgess, Ph.D. >Staff Scientist, Human Connectome Project >Washington University School of Medicine >Department of Psychiatry >Phone: 314-362-7864 >Email: [email protected] > >> On Aug 2, 2016, at 1:42 PM, Chan, Adrian Ka Ho <[email protected]> >>wrote: >> >> Dear HCP experts, >> >> In the "900 subject" release, the rfMRI preprocessed data comes in two >>flavors, for example: >> >> >><SubjectID>/MNINonLinear/Results/rfMRI_REST1_LR_Atlas_MSMALL.dtseries.nii >> and >> >><SubjectID>/MNINonLinear/Results/rfMRI_REST1_LR_Atlas_MSMALL_hp2000_clean >>.dtseries.nii >> >> On the other hand, the tfMRI data seems to be released only in the >>first form (ie, ending with _Atlas_MSMALL.dtseries.nii). Looking at the >>power spectrum, one can see that most of the spikes that are cleared >>away by FIX-ICA in rfMRI also exist in the task data. >> >> The older posts in the mailing list suggest that the task data has not >>been denoised at all since the z-score results do not change much. >>However, instead of the common activation mapping, I would like to >>analyze the time series per se and hope to get rid of as much structured >>noise as possible. Is there a way to remove the equivalent "bad" ICA >>components from the task time series? >> >> Thank you very much for your help (and of course, many thanks also for >>sharing these really high-quality data with all of us)! >> >> Best wishes, >> Adrian >> >> >> >>------------------------------------------------------------------------- >>----------------------- >> >>------------------------------------------------------------------------- >>----------------------- >> Forschungszentrum Juelich GmbH >> 52425 Juelich >> Sitz der Gesellschaft: Juelich >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >> Prof. Dr. Sebastian M. Schmidt >> >>------------------------------------------------------------------------- >>----------------------- >> >>------------------------------------------------------------------------- >>----------------------- >> >> _______________________________________________ >> 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. > >_______________________________________________ >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. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
