Hi Will,

Question 1:
The split-half script generates 2*N sub-folders where N is the number of repitions. For each subfolder you have to call the mica command in order to calculate mICA for that random subgroup.
In your example, those subfolders should lie in $working_dir/results/out_50

Step 2 should be like that:

export MICADIR=/Users/wasimkhan/Documents/mICA_Toolbox

Then start the following command for each sample 1-50 and each group 1-2:

./mica $working_dir/input_list $working_dir/results/out_50/sample_XX/groupXX_input.txt $working_dir/results/out_50/sample_XX/groupXX 2,4,6,8,10 -mask $working_dir/masks/PCC_and_Precuneus_mask_thr20_Harvard.nii.gz -extra -a concat -- sep_vn --nobet --bgthreshold=10 --tr=1 --report --mmthresh=0.5 --Oall

I guess performing the previous steps as suggested here will allow py/ic_corr.py be able to calculate the reproducibilty.

Let me know if it works.

Best,
Tawfik