Hi Andy,

If you have 400 images and are deleting the first 11 your entry in batch_list.txt should be:

'11 399 389 2.01'

i.e., you start with 400 volumes and remove 11, that leaves you with 389 volumes...

It is weird though that the global.1D files is completely empty. Is the global_mask.nii.gz file ok? If you open it, does it cover the full brain?

Maarten