You can do something like this (assuming your seed masks are called mask<n>.nii.gz and you used them in order 1-12):

addpath([getenv('FSLDIR') '/etc/matlab']);

M1=full(spconvert(load('fdt_matrix1.dot')));

M=zeros(12);

fi=1;

for i=1:12

ni=length(find(read_avw(['mask' num2str(i)])));

fj=1;

for j=1:12

nj=length(find(read_avw(['mask' num2str(j)])));

M(i,j) = sum(sum(M1(fi:fi+ni-1,fj:fj+nj-1)));

fj=fj+nj;

end

fi=fi+ni;

end

Cheers,

Saad

On 31 Jul 2013, at 20:10, avner meoded <[log in to unmask]> wrote:

Hi FSL listmemebers

I am currently applying the probtrackx network mode with matrix 1.
I have multiple masks- 12; when I load the matrix file in matlab the marrix is 1046x1046. My question is how can I arrange this matrix so I can obtain the 12x12 dimensions like the number of the masks
Thanks
Avner

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466 (fax 717)