See responses below.
On Wed, Dec 25, 2013 at 2:06 AM, Philip Lin <[log in to unmask]> wrote:
> Hi Watson and McLaren, thanks for your responses, it helps me understand
> more.
>
> After the checking, I've found that the value read by
> spm_read_vols(SPM.xY.VY) is scaled, the scaled value is in pinfo.
>
> 1. I am curious why these voxel values should be scaled ?
>
>>> They are scaled to make the constant term in the GLM approximately 100.
> 2. How this scale be calculated ?
The scale is calculated by spm_fmri_spm_ui.m:
fprintf('%-40s: ','Mapping files') %-#
VY = spm_vol(SPM.xY.P);
fprintf('%30s\n','...done') %-#
%-check internal consistency of images
%--------------------------------------------------------------------------spm_check_orientations(VY);
%-place in xY
%--------------------------------------------------------------------------
SPM.xY.VY = VY;
%-Compute Global variate
%========================================================GM = 100;
q = length(VY);
g = zeros(q,1);
fprintf('%-40s: %30s','Calculating globals',' ') %-#
for i = 1:q fprintf('%s%30s',repmat(sprintf('\b'),1,30),sprintf(
'%4d/%-4d',i,q))%-#
g(i) = spm_global(VY(i));
end
fprintf('%s%30s\n',repmat(sprintf('\b'),1,30),'...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);
end
%-place global variates in global structure
%--------------------------------------------------------------------------
SPM.xGX.rg = g;
SPM.xGX.GM = GM;
SPM.xGX.gSF = gSF;
> Because I've tried many packages in R (nifti / fmri / AnalyzeFMRI) and
> voxel values read by these packages are unscaled. Is there any difference
> to analyze data with scaled and unscaled voxels ?
>
> (values from spm_read_vols) = (values from R packages)*(scale number in
> pinfo)
>
As I stated before, if you use spm_read_vols(spm_vol(actual file names)),
rather than spm_read_vols on the xY structure, then you'd get the same
values as the other programs.
>
> I've tried to check spm_slice_vol.m, but it seems be complied in .mex file
> and I can't see the origin code.
>
> Thanks for your help, sincerely
>
> Philip Lin
>
> On Tue, 24 Dec 2013 13:14:35 -0600, MCLAREN, Donald <
> [log in to unmask]> wrote:
>
> >There are likely two differences:
> >(1) When you display things in SPM, the values are interpolated, turning
> >the interpolation off should fix the issue if you told the program to
> >display the same image that you loaded;
> >(2) SPM.xY.VY.pinfo is likely different from hdr.pinfo, when its created
> >from hdr=spm_vol(filename). The pinfo field contains scaling information.
> >The pinfo field is modified during the 1st level model creation to make
> the
> >mean 100. Thus, it will give you different values than the unscaled image.
> >
> >Hope this helps.
> >
> >Best Regards, Donald McLaren
> >=================
> >D.G. McLaren, Ph.D.
> >Research Fellow, Department of Neurology, Massachusetts General Hospital
> and
> >Harvard Medical School
> >Postdoctoral Research Fellow, GRECC, Bedford VA
> >Website: http://www.martinos.org/~mclaren
> >Office: (773) 406-2464
> >=====================
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> >
> >On Tue, Dec 24, 2013 at 12:21 PM, Chris Watson <
> >[log in to unmask]> wrote:
> >
> >> How are they different?
> >>
> >> On 12/24/2013 09:40 AM, Philip Lin wrote:
> >>
> >> Hi all,
> >>
> >> I have a question about voxel values in SPM. If I read an image into
> SPM8 and use GUI (Display) to show the target image, the value for each
> voxel means intensity. If I read the same image by using
> spm_read_vols(SPM.xY.VY), the values for each voxel is apparently different
> to intensity. What's the difference between them ? What's the meaning of
> values from spm_read_vols ?
> >>
> >>
> >> Thanks if there's any help, sincerely
> >>
> >> Philip Lin
> >>
> >>
> >>
> >>
> >
>
>
>
