> sorry about probably sending my request again, but i did get a message,
> that my post has not been send to the list.
If you look closer, you will see that it has been successfully distributed to
the SPM list (2602 recipients).
>
> i am interested in reanalyzing a set of vbm data with the DARTEL approach.
> the chapter of john ashburner has been very helpful to get through the
> steps, but still a few questions are unanswered. former posts in the list
> are not helpful because they were to technical for me. so maybe there is
> help on a basic level?
>
> 1. 2 of my t1.nii images are not very good realigned in native space.
> without being very familiar with the correct terms (pitch, roll,yaw) the
> axial slices seem to be tilted about +10 degree from the sagital line (i
> assume this to be yaw?). i guess it should be better to realign these
> images before including into the process? i tried a bit with the display
> tool in spm5, playing around with the yaw section but was not able to tilt
> the images in the right direction. any suggestion about where (pitch, roll,
> yaw) i should enter what for a tilt of 10 degree?
10 degrees should be close enough for the initial affine registration to work.
Rotations are in radians, so try values around +/- 0.1745, I think in the yaw
(rotation about z-axis) direction.
>
> 2. as far as i understood it right, the resulting smwrc1*-images are all
> "warped" into the average shape and size and to this related already
> warped? if i want them to be normalized into mni space i should follow the
> steps in john's script 1.2 and 1.2.2. do i have to smooth them again or
> warp them or anything else after these steps? i did not understand the
> posts in the list about that topic.
For VBM, it is a bit of a hassle to have to compose all the deformations
together in order to get your results into MNI space. I suggest that you try
the following...
Generate a Template_6_sn.mat by using the Normalise button to do an spatial
normalisation of Template_6.nii,1 with the tpm/grey.nii image in the spm
distribution. The resulting Template_6_sn.mat will contain an affine
transform that could be used to bring the dartel warped images into MNI
space. The easiest thing to do then is to modify the headers of the images
that have been spatiallly normalised to the DARTEL average by pasting the
following text into MATLAB, and selecting the appropriate files:
% 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
>
> 3. after normalization into mni space, the resulting images look strange,
> somewhat frayed on the cortical edges. they look much worse than the former
> images. what happened?
I'm not sure.
Best regards,
-John
