Dear Alfonso,

The conn-module command we used is the following:
conn_module( 'glm' , ...
'data', 'med100sujetsp.mtx.nii', ...
'design_matrix', X, ...
'contrast_between', C, ...
'folder', 'C:\Users\laurence\Documents\MATLAB\ ron\' );
We played a bit with the design and contrast matrices but to no avail. We still get the message that there is a mismatch in the number of subjects in the design matrix. I attach the design matrix and one of the contrasts we tried. The 50 first columns in the design matrix are for the rsfMRI data of session 1, the next 50 are related to the second rsfMRI condition (X). The first 50 lines in our data matrix (mtx.nii) refer to our 50 subjects in condition 1, the next 50 lines refer to the same subjects in condition 2. Our aim is to perform a paired t-test (50 subjects, tested in 2 conditions). We tried various possible contrasts but they all gave the same error message.