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Dear Guillaume,

2016-01-05 16:14 GMT+01:00 Guillaume Flandin <[log in to unmask]>:

Dear Matthieu,

On 04/01/16 12:01, Matthieu Vanhoutte wrote:
> 1) If I well understood, when using global normalization with
> proportional scaling the overall grand mean scaling is always used with
> GM = 50 per default ? (l. 803)

unless you specify a different value in:
Global normalisation > Overall grand mean scaling > Yes > Grand mean
scaled value
It will then be used to define variable GM at l.795 or l.801.

> 2) I couldn't find, in case of a user-defined global calculation, where
> this user-defined factor is divided/applied on the image ?

If you specify your own global effects values in:
Global calculation > User > Global values
they will then be used to define variable g at l.750. This variable is
then used to define the global scaling factor gSF and applied to the
data, as mentioned before, at l.855.

In this case I see effectively that user defined global value is used to define g at l.750. But in this case, iGMsca = 9 and the definition of global scaling factor gSF is then gSF = ones(nScan,1) at l.847. So, I don't see where user-defined global value g is taken into account at l.855 ?

Moreover, at l.855 VY(i).pinfo(1:2,:) structure is modified but when I tried to write the new image rescaled with spm_write_vol the intensities haven't changed compared to initial image. Do I have to also multiply each voxel intensity by pinfo(1,1) to take into account intensity normalization ?

Best regards,

Matthieu

All this code dates apparently from SPM99.

Best regards,
Guillaume.

> Best regards,
>
> Matthieu
>
> 2015-12-18 17:52 GMT+01:00 Guillaume Flandin <[log in to unmask]
> <mailto:[log in to unmask]>>:

>
> Dear Matthieu,
>
> the function you are looking at concerns first level fMRI so for PET
> 'basic' models, you need to look at
> spm12/config/spm_run_factorial_design.m
> When using proportional scaling global normalisation, the global scaling
> factor, gSF, is computed l.838 and applied to the data l.855.
>
> Best regards,
> Guillaume.
>
>
> On 18/12/15 15:33, Matthieu Vanhoutte wrote:
> > Dear SPM experts,
> >
> > I have been searching for explicit formula of the global normalization
> > with proportional scaling as it is used in SPM. I have found this code
> > in "spm_fmri_spm_ui.m" :
> >
> > /%-Compute Global variate
> >
> %==========================================================================
> > GM = 100;
> > q = length(VY);
> > g = zeros(q,1);
> > fprintf('%-40s: ','Calculating globals')
> %-#
> > spm_progress_bar('Init',q,'Calculating globals');
> > if spm_mesh_detect(VY)
> > for i = 1:q
> > dat = spm_data_read(VY(i));
> > g(i) = mean(dat(~isnan(dat)));
> > spm_progress_bar('Set',i)
> > end
> > else
> > for i = 1:q
> > g(i) = spm_global(VY(i));
> > spm_progress_bar('Set',i)
> > end
> > end
> > spm_progress_bar('Clear');
> > fprintf('%30s\n','...done')
> %-#
> >
> > %-Scale if specified (otherwise session specific grand mean scaling)
> >
> %--------------------------------------------------------------------------
> > gSF = GM./g;
> > if strcmpi(SPM.xGX.iGXcalc,'none')
> > for i = 1:nsess
> > gSF(SPM.Sess(i).row) = GM./mean(g(SPM.Sess(i).row));
> > end
> > end
> >
> > %-Apply gSF to memory-mapped scalefactors to implement scaling
> >
> %--------------------------------------------------------------------------
> > for i = 1:q
> > SPM.xY.VY(i).pinfo(1:2,:) = SPM.xY.VY(i).pinfo(1:2,:) * gSF(i);
> > if spm_mesh_detect(VY)
> > SPM.xY.VY(i).private.private.data{1}.data.scl_slope = ...
> > SPM.xY.VY(i).private.private.data{1}.data.scl_slope *
> gSF(i);
> > SPM.xY.VY(i).private.private.data{1}.data.scl_inter = ...
> > SPM.xY.VY(i).private.private.data{1}.data.scl_inter *
> gSF(i);
> > else
> > SPM.xY.VY(i).private.dat.scl_slope = ...
> > SPM.xY.VY(i).private.dat.scl_slope * gSF(i);
> > SPM.xY.VY(i).private.dat.scl_inter = ...
> > SPM.xY.VY(i).private.dat.scl_inter * gSF(i);
> > end
> > end
> >
> > %-Place global variates in xGX
> >
> %--------------------------------------------------------------------------
> > SPM.xGX.sGXcalc = 'mean voxel value';
> > SPM.xGX.sGMsca = 'session specific';
> > SPM.xGX.rg = g;

> > SPM.xGX.GM <http://SPM.xGX.GM> <http://SPM.xGX.GM> = GM;

> > SPM.xGX.gSF = gSF;
> > /
> > /-------------------------------------/
> >
> > I understood global mean is computed in "g" variable but didn't see
> > where it is used after on the data volume in case of proportional
> scaling ?
> >
> > Is the formula simply divided each intensity voxel of the image
> per the
> > global mean "g" ?
> >
> > Best regards,
> > Matthieu
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG
>
>

--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG