Yes I think that's it. Cheers.
> On 22 Nov 2016, at 04:20, Harms, Michael <[email protected]> wrote: > > > Isn’t it more like (data/4DMean*10000), so that the percentage change > relative to the mean is preserved? > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: <[email protected] > <mailto:[email protected]>> on behalf of "Glasser, > Matthew" <[email protected] <mailto:[email protected]>> > Date: Monday, November 21, 2016 at 9:53 PM > To: mali s <[email protected] <mailto:[email protected]>>, > NEUROSCIENCE tim <[email protected] <mailto:[email protected]>> > Cc: "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > Subject: Re: [HCP-Users] 4D Intensity normalization in the fMRIVolume pipeline > > We didn’t do global signal regression or mean stabilization if that is what > you are wondering about. The formula is essentially (data – 4DMean) + 10000. > > Peace, > > Matt. > > From: mali s <[email protected] <mailto:[email protected]>> > Date: Monday, November 21, 2016 at 9:49 PM > To: Timothy Coalson <[email protected] <mailto:[email protected]>> > Cc: Matt Glasser <[email protected] <mailto:[email protected]>>, > "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > Subject: Re: [HCP-Users] 4D Intensity normalization in the fMRIVolume pipeline > > We are doing connectivity analysis on this data, and it is important for us > to understand the exact formula used to convert to the intensity normalized > image. It would really help if you can share this or guide me to a link where > I can find the details. > > To put it precisely, let's say I have r(x,y,z,t) after all the preprocessing > steps, and just before the intensity normalization. What is the formula used > to convert this to the intensity normalized image n(x,y,z,t) ? > > Regards, > Mali > > > On Tue, Nov 22, 2016 at 8:44 AM, Timothy Coalson <[email protected] > <mailto:[email protected]>> wrote: >> 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] >> <mailto:[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] >>> <mailto:[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] >>>> <mailto:[email protected]>> on behalf of mali s >>>> <[email protected] <mailto:[email protected]>> >>>> Date: Monday, November 21, 2016 at 8:08 PM >>>> To: "[email protected] <mailto:[email protected]>" >>>> <[email protected] <mailto:[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] <mailto:[email protected]> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> <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] <mailto:[email protected]> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> > > > > -- > Mali Sundaresan > > > 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] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <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 --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
