`filterwarnings = ["error"]` triggered a some improvements needed

[htwangtw]

          okay adding those extra options has raised some issues and revealed some very hacky things I did for good - 

• test_load_atlas_setting, test_generate_group_mask: i manually override the templateflow home to load customised atlas. this is not a typical use case of templateflow
• test_calculate_intranetwork_correlation: we used the niftimasker to flatten label atlas (3D); solvable
• test_get_bids_images: this is from a hack to force pybids to index fmriprep outputs, you are a better person to judge if i am doing the right thing here

Originally posted by @htwangtw in #58 (comment)

After the above issues are fixed, filterwarnings = ["error"] should be add to the pytest config

[htwangtw]

This will trigger a lot of upstream projects with deprecation warnings. Skip for now.