Hi Doug/freesurfers,

I am now trying to make a mask that includes only positively activated voxels for one conditon versus passive viewing (ConditionAvspassive).

Using the inputs that you suggested, I ran the following command:

mri_binarize --i ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive/ces.nii.gz --o ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive_mask.ces.nii.gz --mask-thresh 0.00001 --min 0.00001

So my understanding of what this should be doing is making a mask that only includes positively activated voxels compared to passive viewing. However, if you see the attached images of both the mask that this command creates, and the activation maps of ConditionAvpassive (set at a very low threshold for visualization purposes), you can see that there are several regions that are included in the mask that are in fact deactivated compared to passive viewing.

Is there something wrong with the command that I'm running that is causing this to happen?

Thank you for any insight!

Maya