central = Interface('https://central.xnat.org', 'schwarty', 'plopplop',
'/havoc/store/xnat')
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
input_files = [central.select('/project/Volatile/resources/123150742/files/000075760021s002a1001.nii.gz').get()]
# where put files arguments?
# extract_ref = partial(mem.cache(fsl.ExtractROI), t_min=42, t_size=1)
nosestrip = partial(mem.cache(fsl.BET), frac=0.3)
skullstrip = partial(mem.cache(fsl.BET), mask=True)
refskullstrip = partial(mem.cache(fsl.BET), mask=True)
# coregister = mem.cache(fsl.FLIRT)(dof=6)
# extract_ref_exec = [
# extract_ref(in_file=in_file) for in_file in input_files]
nosestrip_exec = [
nosestrip(in_file=in_file) for in_file in input_files]
skullstrip_exec = [
skullstrip(in_file=o.outputs.out_file) for o in nosestrip_exec]
refskullstrip_exec = [
refskullstrip(in_file=o.outputs.out_file) for o in skullstrip_exec]
mem.clear_previous_runs()
