I know, but the ROI file I am using (Clust_mask_0001+tlrc) contains only one ROI, it was made by [Write]'ing one specific cluster from GUI's clustering report.
Either way, if I use the ordered mask (-omask) mode on this single-ROI file, or ordered mask on a multi-ROI file, I get the same numbers on this ROI and regions: 41.8% and 32.3%, vs. 45.2% and 34.8% from doing it step by step or in Matlab
whereami -atlas 'ARM Level 3' -omask Clust_mask_0001+tlrc
++ Input coordinates orientation set by default rules to RAI
++ In ordered mode ...
++ Have 2 unique values of:
0 1
++ Skipping unique value of 0
++ ========================================================================
++ Processing unique value of 1
++ 5519 voxels in ROI
++ 43959 voxels in atlas-resampled mask
Intersection of ROI (valued 1) with atlas ARM Level 3 (sb0):
41.8 % overlap with CR_dlPFC
[CR_dorsolateral_prefrontal_cortex], code 554
32.3 % overlap with CR_ACC
[CR_anterior_cingulate_cortex], code 503
[...]
91.5 % of cluster accounted for.
whereami -atlas 'ARM Level 3' -omask Clust_mask+tlrc
++ Input coordinates orientation set by default rules to RAI
++ In ordered mode ...
++ Have 4 unique values of:
0 1 2 3
++ Skipping unique value of 0
++ ========================================================================
++ Processing unique value of 1
++ 5519 voxels in ROI
++ 43959 voxels in atlas-resampled mask
Intersection of ROI (valued 1) with atlas ARM Level 3 (sb0):
41.8 % overlap with CR_dlPFC
[CR_dorsolateral_prefrontal_cortex], code 554
32.3 % overlap with CR_ACC
[CR_anterior_cingulate_cortex], code 503
[...]
-----
91.5 % of cluster accounted for.
