There are two matrices in the image headers. One represents a full
12-parameter affine transform, whereas the other only uses 9 parameters. SPM
usually (except for imported DARTEL images, and flow fields) sets both
matrices to be the same, and generally only reads the full 12 parameter
representation. If the 12-parameter matrix can not be exactly represented by
9 parameters, then you receive the warning message to show that one of the
matrices can only be approximately represented. In this case, the warnings
should not matter, as SPM will only read orientation information from the
exact matrix.

Best regards,
-John


On Wednesday 04 June 2008 12:14, Xiaochen Hu wrote:
> Dear all,
>
> I had another question which is related to issue of the modulating
> images into MNI space.
> I have used the method that MCLAREN Donald has proposed, but after
> that, I tried to smooth the mmwrc*.* images, I got following warning:
>
> Warning: QFORM0 representation has been rounded.
>
> > In @nifti/private/encode_qform0 at 27
>
> In nifti.subsasgn>fun at 109
> In nifti.subsasgn at 20
> In spm_create_vol>create_vol at 81
> In spm_create_vol at 16
> In spm_smooth at 110
> In spm_config_smooth>smooth at 79
> In spm_jobman>run_struct1 at 1585
> In spm_jobman>run_struct1 at 1595
> In spm_jobman>run_struct1 at 1595
> In spm_jobman>run_struct at 1514
>
> is that normal?
>
> best regards,
> Xiaochen
>
> Am Montag, den 02.06.2008, 19:26 +0530 schrieb Harsha N Halahalli:
> > Thanks Donald for those explicit steps. This would definitely be of
> > great help.
> >
> > Best Regards
> > Harsha
> >
> > On Mon, Jun 2, 2008 at 7:12 PM, MCLAREN, Donald
> > <[log in to unmask]> wrote:
> > To normalize to MNI space:
> >
> > (1) Estimate the transform of the GM tissue segment (template
> > 6,
> > volume 1) to GM prior in the spm/apriori; set the nonlinear
> > iterations
> > to 0 and nonlinear frequency to Inf.
> > (2) Make a m-file containing John's code. The line:
> > Ni.dat.scl_slope =
> > Ni.dat.scl_slope*scale; does the modulation.
> > (3) Run the m-file on your mwrc* files. This should be the
> > output of
> > the create warped step.
> > (4) Make special note of which files have been run through the
> > m--file
> > as the file name will not change, but the values and .mat
> > elements
> > will change. You might want to copy the files to mmwrc* files
> > first to
> > be know that they have been modulated twice.
> >
> > Hope that helps.
> >
> >
> > On Mon, Jun 2, 2008 at 8:25 AM, Harsha N Halahalli
> >
> > <[log in to unmask]> wrote:
> > > Dear Dr. John Ashburner,
> > > Actually I had seen that post that you have referred to but
> >
> > being a bit of a
> >
> > > dummy to VBM did not really understand the discussion
> >
> > there :(
> >
> > > I know there are constraints on your time, but if I could
> >
> > get a bit of an
> >
> > > explanation, I would indeed be grateful.
> > > Thanks.
> > >
> > > Best Regards
> > > Harsha
> > >
> > > On Mon, Jun 2, 2008 at 7:29 PM, John Ashburner
> >
> > <[log in to unmask]>
> >
> > > wrote:
> > >> Here is an old posting that may help...
> >
> >
> > -----------------------------------------------------------------------
> >
> > >> > In the user guide it states that the DARTEL results are
> >
> > not in MNI space
> >
> > >> > and they need to be transformed to MNI space using a
> >
> > linear affine
> >
> > >> > transformation. And then create a composite transform
> >
> > from the flow
> >
> > >> > field
> > >> > and the _sn.mat file. However, when I do this and apply
> >
> > them to the rc*
> >
> > >> > images, I get severly warpped brains that are nowhere
> >
> > close to MNI
> >
> > >> > space.
> > >> > Interestingly, when I use the c* images that have the
> >
> > tissue classes in
> >
> > >> > native space, everything works.
> > >> >
> > >> > (1) Am I doing something wrong or when I apply the
> >
> > composite
> >
> > >> > transformation
> > >> > does it need to be applied to the native space images?
> > >>
> > >> I think I got the documentation correct, although I am
> >
> > reluctant to run
> >
> > >> through all the processing steps again to check that there
> >
> > are no typos.
> >
> > >> > (2) y* files are created when you create the composite
> >
> > transformation,
> >
> > >> > can
> > >> > I use these images to calculate the jacobian determinant?
> >
> > If yes, can I
> >
> > >> > use
> > >> > i1.*i2 in IMCALC to create a modulated image?
> > >>
> > >> I'm guessing that you are doing a VBM study. The original
> >
> > intention was
> >
> > >> to
> > >> superimpose the blobs on to the template that DARTEL
> >
> > generates, but I
> >
> > >> guess
> > >> you want to report your results as coordinates in MNI
> >
> > space.
> >
> > >> > (3) In using a composite transformation and applying the
> >
> > the jacobian in
> >
> > >> > MNI space, only one transformation is necessary, rather
> >
> > than 2 if the
> >
> > >> > jacobains are applied in DARTEL space and then normalized
> >
> > to MNI space.
> >
> > >> > This seems preferable as there is less resampling of the
> >
> > data this way;
> >
> > >> > or
> > >> > am I missing a critical step in the process?
> > >>
> > >> For VBM, it may be easier to tweek the headers of the
> >
> > DARTEL warped
> >
> > >> images, so
> > >> that the affine transform in the headers is modified...
> > >>
> > >>
> > >>
> > >> % Select files
> > >> PN = spm_select(1,'.*_sn.mat','Select sn.mat file');
> > >> PI = spm_select(inf,'nifti','Select images');
> > >>
> > >> % Determine affine transform from header
> > >> sn = load(deblank(PN));
> > >> M = sn.VG(1).mat/(sn.VF(1).mat*sn.Affine);
> > >>
> > >> % Scaling by inverse of Jacobian determinant, so that
> > >> % total tissue volumes are preserved.
> > >> scale = 1/abs(det(M(1:3,1:3)));
> > >>
> > >> % Pre-multiply existing headers by affine transform
> > >> for i=1:size(PI,1),
> > >>
> > >> % Read header
> > >> Ni = nifti(deblank(PI(i,:)));
> > >>
> > >> % Pre-multiply existing header by affine transform
> > >> Ni.mat = M*Ni.mat;
> > >> Ni.mat_intent='MNI152';
> > >>
> > >> % Change the scalefactor. This is like doing a
> >
> > "modulation"
> >
> > >> Ni.dat.scl_slope = Ni.dat.scl_slope*scale;
> > >>
> > >> % Write the header
> > >> create(Ni);
> > >> end
> > >>
> > >>
> > >>
> > >> Note that the original affine voxel-to-world mappings are
> >
> > still saved in
> >
> > >> the
> > >> header (Ni.mat0).
> > >>
> > >> Best regards,
> > >> -John
> >
> >
> > -----------------------------------------------------------------------
> >
> > >> On Monday 02 June 2008 06:27, Harsha Halahalli wrote:
> > >> > Dear SPMers
> > >> >
> > >> > I am attempting to use the DARTEL toolbox for a VBM type
> >
> > analysis. I
> >
> > >> > have
> > >> > been able to follow the guidelines in the excellent
> >
> > manual (that John
> >
> > >> > Ashburner has kindly made available here)to obtain flow
> >
> > fields and
> >
> > >> > warped
> > >> > tissue class images in the "averaged" space.
> > >> > I am now trying to spatially normalize the tissue images
> >
> > to the MNI
> >
> > >> > space.
> > >> > I understand that the approach involves estimating the
> >
> > parameters for
> >
> > >> > affine normalization of the dartel tissue template with
> >
> > the MNI tissue
> >
> > >> > probability map and combining this with the dartel
> >
> > generated flow fields
> >
> > >> > to
> > >> > obtain composite deformations. I have a few questions
> >
> > about these steps:
> > >> > 1. Which are the images to which we are to apply the
> >
> > composite
> >
> > >> > deformations. I have applied them to the rc*.nii images.
> >
> > Is this
> >
> > >> > correct?
> > >> > 2. The resulting MNI normalized images do not appear to
> >
> > be "modulated".
> >
> > >> > How
> > >> > would I go about obtaining "modulated" images in the MNI
> >
> > space?
> >
> > >> > Any assistance would be greatly appreciated.
> > >> >
> > >> > Harsha
> > >> >
> > >> > -------------------------------
> > >> > Harsha Halahalli
> > >> > Research Associate
> > >> > MBIAL, Department of Psychitary
> > >> > National institute of Mental Health and Neuro Sciences
> >
> > (NIMHANS)
> >
> > >> > Bamgalore - 560029, INDIA
> >
> > --
> > Best Regards, Donald McLaren
> > =====================
> > D.G. McLaren
> > University of Wisconsin - Madison
> > Neuroscience Training Program
> > Tel: (773) 406 2464
> > =====================
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