import pandas as pd

from nipype.interfaces.freesurfer import Binarize

from nipype.interfaces.io import SelectFiles

subjects = pd.read_csv('/scr/ilz3/myelinconnect/subjects.csv')

subjects=list(subjects['DB'])

subjects.remove('KSMT')

labels= [11, 12, 13, 16, 18] + range(30,42)

templates={'seg': '/scr/ilz3/myelinconnect/struct/seg/{subject}*seg_merged.nii.gz'}

mask_file = '/scr/ilz3/myelinconnect/struct/myelinated_thickness/subcortex_mask/%s_subcortical_mask.nii.gz'

for subject in subjects:

select = SelectFiles(templates)

select.inputs.subject = subject

select.run()

seg_file = select.aggregate_outputs().seg

binarize = Binarize(match = labels,

out_type = 'nii.gz')

binarize.inputs.binary_file = mask_file%subject

binarize.inputs.in_file=seg_file

binarize.run()