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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 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. 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