Hi Alfonso and CONN Users,
 
I've created intensity basked masks for participant's fMRI data to exclude parts of the brain with signal loss (e.g., OFC) from analysis. Each participant has their own mask. Now, I would like to apply these to individuals within CONN (or before uploading in CONN) to conduct analyses on data within the masks. Is this an option within CONN and/or can someone advise me how to do this?

Thanks so much

Hi Alexandra,

One option would be to run the preprocessing step 'functional_mask' to mask your functional data (set to 0's all functional data outside the mask). For ROI-based analyses, that will effectively remove those voxels from consideration in a subject-specific manner (as 0-values in the BOLD data will be disregarded when importing subject-specific ROI timeseries). For voxel-based timeseries, though, the effect is probably the same as constructing the intersection of all those subject-specific masks and defining a common analysis mask based on that (as voxel-based second-level analyses cannot handle different missing-data across different voxels, so they instead will simply remove voxels list-wise in the presence of missing data)

Hope this helps
Alfonso
 
Originally posted by Alexandra Muratore: