Hi, Matthew.  Are you talking about white matter lesions or gray matter?  The aCompCor method in CONN regresses out white matter and CSF from the functional connectivity signal as part of the denoting process.  As long as white matter lesions are not being falsely segmented as gray matter, then you shouldn't have any problems.  I know that CAT12 has options to detect and either reassign white matter lesions as white matter or as its own tissue class.  In theory, though I haven't tried it yet, you should be able to import the CAT12 white matter segmentations (those with lesions assigned to white matter) into CONN at the setup stage.  This should allow any lesion-related signal to be regressed out with the normal white matter during the denoising stage.  

If, on the other hand, you are talking about gray matter lesions or encephalomalacia, then there I believe you will need to alter the analysis brain mask in the setup options.  I haven't come upon this problem yet in our patient data, so I really can't speak to how to implement that change in CONN.  Using the example above with the tissue segmentations, I guess one could assign a lesion area to the white matter or CSF tissue type mask for that person, which (I think) would exclude that lesioned gray matter area from contributing to the non-regressed signal.  

Hope this helps, though admittedly I'm a bit shaky on the correction possibilities myself (other than how we handle the white matter lesions).

Warm regards,
Jeff



Originally posted by Matthew Heard: