Hi there,

I'm doing ROI-to-ROI correlation and gPPI connectivity 2nd level analyses using TFCE with subject-specific ROIs. The issue is that some subjects are missing some ROIs (we are interested in some small frontal ROIs that are difficult to localizer reliably in all subjects.) 

As others have mentioned, Conn will exclude an ROI from the analysis if it is not present in all subjects. The workaround mentioned here (https://www.nitrc.org/forum/message.php?...) is to make arbitrary ROIs for the missing ones, then exclude the subjects with missing ROIs from the 2nd level analysis. But because TFCE analyses all ROI-to-ROI connections together, this would exclude a subject even if they have 25 out of our 26 ROIs - which throws away a lot of data. 

Is there any way to allow for missing ROIs in this context without removing full subjects or full ROIs from the analysis?

One thing I tried was to manually replace the arbitrary ROI data for the missing ROIs with NaNs in the Z and SE variables of the relevant */results/firslevel/gPPI/resultsROI_Condition001.mat file. But it seems that 2nd level analyses (TFCE at least) just removes rows/cols that are NaNs and this results in a dimensions error when it tries to concatenate all the matrices for each ROI.

Thank you.

Best,

Tom from BU