Convert from FSL format

[paula...@gmail.com]

Dear all,

We are trying to convert the output files  from BedpostX (FSL) to DSI studio format using the following code below but we got this error message: ???subscripted assignment dimension  mismatch. Error in ==>FSL_to_DSI at 16

fib.dir0(1,:,:,:) = sin(theta1.img).*cos(phi1.img);

Does anyone know how to solve this?

Thanks!

Best,

Paula

 

% You may need to download a nifti file loader to run this function.

% http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

% This example shows converting a maximum of 2 fiber populations. 

% For populations more than 2, you may need to modify the codes.




theta1 = load_untouch_nii('mean_th1samples.nii.gz');

theta2 = load_untouch_nii('mean_th2samples.nii.gz');

phi1 = load_untouch_nii('mean_ph1samples.nii.gz');

phi2 = load_untouch_nii('mean_ph2samples.nii.gz');

f1 = load_untouch_nii('mean_f1samples.nii.gz');

f2 = load_untouch_nii('mean_f2samples.nii.gz');

fib.dimension = size(f1.img);

fib.voxel_size = f1.hdr.dime.pixdim(2:4);

fib.fa0 = double(reshape(f1.img,1,[]));

fib.fa1 = double(reshape(f2.img,1,[]));

fib.dir0(1,:,:,:) = sin(theta1.img).*cos(phi1.img);

fib.dir0(2,:,:,:) = sin(theta1.img).*sin(phi1.img);

fib.dir0(3,:,:,:) = cos(theta1.img);

fib.dir1(1,:,:,:) = sin(theta2.img).*cos(phi2.img);

fib.dir1(2,:,:,:) = sin(theta2.img).*sin(phi2.img);

fib.dir1(3,:,:,:) = cos(theta2.img);

fib.dir0 = double(reshape(fib.dir0,3,[]));

fib.dir1 = double(reshape(fib.dir1,3,[]));




% flip xy: you may need to make sure that this orientation is correct

fib.fa0 = reshape(fib.fa0,fib.dimension);

fib.fa0 = fib.fa0(fib.dimension(1):-1:1,fib.dimension(2):-1:1,:);

fib.fa0 = reshape(fib.fa0,1,[]);

fib.fa1 = reshape(fib.fa1,fib.dimension);

fib.fa1 = fib.fa1(fib.dimension(1):-1:1,fib.dimension(2):-1:1,:);

fib.fa1 = reshape(fib.fa1,1,[]);

fib.dir0 = reshape(fib.dir0,[3 fib.dimension]);

fib.dir0 = fib.dir0(:,fib.dimension(1):-1:1,fib.dimension(2):-1:1,:);

fib.dir0(3,:,:,:) = -fib.dir0(3,:,:,:);

fib.dir0 = reshape(fib.dir0,3,[]);

fib.dir1 = reshape(fib.dir1,[3 fib.dimension]);

fib.dir1 = fib.dir1(:,fib.dimension(1):-1:1,fib.dimension(2):-1:1,:);

fib.dir1(3,:,:,:) = -fib.dir1(3,:,:,:);

fib.dir1 = reshape(fib.dir1,3,[]);

save('out.fib', '-struct','fib','-v4');

[Fang-Cheng Yeh]

Hi Paula,

Can you check out the "size" of theta1.img and phi1.img ?

e.g. what is the output of size(theta1.img) ? and size(phi1.img)?

Best regards,
Frank

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