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
m 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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