Integrate CNN brain masking

[tashrifbillah]

Algorithm:

with TemporaryDirectory() as tmpdir, local.cwd(tmpdir):
    tmpdir= local.path(tmpdir)
    
    # dwi is a local.path object
    copy(dwi, tmpdir)
    with open('caselist.txt', 'w') as f:
        f.write(pjoin(tmpdir, dwi.basename))
    
    # subprocess call
    # obtain model_dir from config file
    dwi_masking.py -i caselist.txt -f model_dir
    
    prefix= dwi.basename.split('.nii')[0]
    mv dwib0_{prefix}-multi_BrainMask.nii.gz, dwi.dirname

The above can be inserted here checking mask_method.lower()=='cnn' condition.

[tashrifbillah]

CnnMask task accepts dwi, on the other hand BseBetMask task accepts bse. This discrepancy is a challenge for integrating both methods.

A way around can be modifying CNN masking tool to accept bse.

[tashrifbillah]

New flowcharts:

cc @sbouix