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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 > >