Yes, because the 3d volume means were already close to each other even before any normalization.
Tim On Mon, Nov 21, 2016 at 8:56 PM, mali s <[email protected]> wrote: > 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
