Hi Jaron,
Yes, that is perfectly fine, to run second-level analyses of arbitrary ROI-to-ROI connectivity matrices you may:

1) convert first your matrix data to NIFTI format, for example using something like:

   conn_mtx_write('/folder/mydatafile.mtx.nii', Z);

where Z is your ROI-by-ROI-by-subjects 3D matrix containing the connectivity values for each subject. You may also include the ROI labels as well as the ROI spatial locations info to the conn_mtx_write command if you wish, see "help conn_mtx_write" for additional details

2) run your desired group-level analyses, for example using something like:

   conn_module( 'glm' , ...
   'data', '/folder/mydatafile.mtx.nii', ...
   'design_matrix', X, ...
   'contrast_between', C, ...
   'contrast_within', M, ...
   'folder', '/folder/myresults' );

where X is your design matrix, and C/M are the between- and within- subjects contrast, respectively (see https://web.conn-toolbox.org/fmri-method... for details)

and 3) after that, you may display the second-level results using the standard CONN gui options at any time using the syntax:

  conn_display /folder/myresults

Hope this helps
Alfonso


Originally posted by Jaron Kupers: