We are using contrast masking to mask our group comparison contrasts with the two single group contrasts - effectively saying to only compare the two groups when both groups are positive.
We would like to use the option "Mask using z>0 instead of z stats pass thresholding." This option worked for us in an old version of FSL. The problem is that when we re-run the analysis with the latest version of FSL, it appears that it is not using the z>0 option when we select that option. Even though we have told it to mask using z>0, it is masking using z>threshold.
The log entries for both analyses are below. The original, which masked using z>0 reads:
"/Applications/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -d 0.0240846 --volume=243832 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --mm --olmax=lmax_zstat1_std.txt > cluster_zstat1_std.txt"
The re-run, which was supposed to mask using z>0 but instead masked using z>threshold reads:
"/Applications/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.024084 --volume=243832 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --mm --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt"
What is concerning is that the re-run includes "-p 0.05" and the original does not. That is why I think that the re-run in FSL 5 is masking using z>threshold instead of z>0.
Is FSL, in fact, masking with z>threshold when it is told to mask with z>0? If so, is this a bug in FSL 5? Is there a workaround?