Thank you the replies! Tim, I think I understand your explanation. In mathematical terms, it means 4d mean is close to each of the 3d volume means, right?
I'm guessing "PFA" means "please find attached". BOLD scans have a lot of structural signal in them, which we haven't subtracted out - the activation-related signal is a modest local fluctuation compared to this base signal level. Additionally, since you are averaging over the entire brain mask, the activation signals get considerably diluted by white matter, and by gray matter that isn't similarly active at that timepoint. Tim I'm guessing "PFA" means "please find attached". BOLD scans have a lot of structural signal in them, which we haven't subtracted out - the activation-related signal is a modest local fluctuation compared to this base signal level. Additionally, since you are averaging over the entire brain mask, the activation signals get considerably diluted by white matter, and by gray matter that isn't similarly active at that timepoint. Tim I'm guessing "PFA" means "please find attached". BOLD scans have a lot of structural signal in them, which we haven't subtracted out - the activation-related signal is a modest local fluctuation compared to this base signal level. Additionally, since you are averaging over the entire brain mask, the activation signals get considerably diluted by white matter, and by gray matter that isn't similarly active at that timepoint. Tim On Mon, Nov 21, 2016 at 8:14 PM, Glasser, Matthew <[email protected]> wrote: > I don’t know what PFA is and am otherwise having some trouble following > your question. There is grand mean intensity normalization to 10000, > meaning that the entire 4D image inside the brain mask has a mean of 10000. > > Peace, > > Matt. > > From: <[email protected]> on behalf of mali s < > [email protected]> > Date: Monday, November 21, 2016 at 8:08 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] 4D Intensity normalization in the fMRIVolume pipeline > > Dear HCP team, > > We are using minimally preprocessed volume files from HCP database > (100206/MNINonLinear/Results/tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii). The > release notes for this subject say these files were processed using v3+ of > the pipeline. I believe 4d intensity normalization to mean of 10^4 is being > done here. > > However, PFA the mean brain activation (after applying mask) during the > course of the scan . They are all close to 10^4, more like a global signal > normalization for every 3d volume. > > I am having trouble reconciling both. Thanks in advance for the help. > > Regards, > Mali > > > _______________________________________________ > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
