Hi Luis,

You do not necessarily need to rerun DKE to run the FT module. The reason the FT module needs the fa image is the .nii header contains a lot of info that the FT module uses, like the voxel dimensions, image dimensions, and the vox_to_ras transformation in the nifti header. There is a possible solution included below if you have Matlab, which should run in a few seconds. I am not sure if the FT module will run with the output images are from the Skyra, but if they are in .nii format, then it should.

However, I am very surprised that DKE took 5 hours to run on a single subject. This suggests the constrained fitting could be doing more than it should, which can potentially happen if there is an image / gradient miss-match. I would check the parameter maps such as fa and kmean and make sure they look good. Sometimes it can also be beneficial to drop the median filtering method down to 1 or 0 but that won't effect the processing time.

Best,

Russell

%fn_img: file path 'template' image (.nii) (eg b0 3D or 4D)
%fn_dt: file path to DT.mat (.mat)
%fn_fa: file path to new fa image to write (.nii)

hdr = spm_vol(fn_img);
load(fn_dt)
idx = sqrt(sum(DT.^2))>0;
fa = zeros(1,prod(hdr(1).dim(1:3)));
fa(idx) = sqrt(3.*sum([DT(1:3,idx)-repmat(sum(DT(1:3,idx))./3,3,1);repmat(DT(4:6,idx),2,1)].^2)./...
sum([DT(1:3,idx);repmat(DT(4:6,idx),2,1)].^2)./2);
hdr(1).fname = fn_fa;
hdr(1).dt = [16 0];
spm_write_vol(hdr(1),reshape(fa,hdr(1).dim(1:3)));
edit