Hello,

You can use the Import utility in the GUI to achieve what you want. Go to "Project" and click on Import. Then you can select a SPM.mat file. Conn will automatically import the functional images and experimental design from the SPM.mat file along with the realignment (motion) parameters as a first level covariate. You might have to specify the structural files manually (but if you use the "Find" button, it is very efficient and requires minimal effort, as long as you correctly specify the filters).

As an alternate, you could specify the smoothed functional files as primary data set and the normalized functional files as the secondary data set. Normalized skull stripped images are usually specified in the structural files tab but it does not matter too much (structural files are only used for display purposes during denoising and first level; if they are normalized, you should be fine). You would have to specify the rp_*.txt file for each subject as a first level covariate.

I would suggest going about the first method as it i much more convenient. Do check your overall experiment design and other parameters before proceeding further (for example when importing SPM.mat file into a new project, you might have to delete the "rest" condition).

Finally, you might want to run the outlier detection from preprocessing tab before proceeding to denoising.


Hope this helps


Best
Pravesh