def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat_image = rp[R('T1w', label='reorient')]
anat_skullstrip = NipypeJob(interface=afni.SkullStrip(
outputtype='NIFTI_GZ',
args=create_3dskullstrip_arg_string(**config)),
reference='anat_skullstrip')
anat_skullstrip.in_file = anat_image
anat_brain_mask = NipypeJob(interface=afni.Calc(expr='step(a)',
outputtype='NIFTI_GZ'),
reference='anat_brain_mask')
anat_skullstrip_orig_vol = NipypeJob(
interface=afni.Calc(expr='a*step(b)', outputtype='NIFTI_GZ'),
reference='anat_skullstrip_orig_vol')
anat_brain_mask.in_file_a = anat_skullstrip.out_file
anat_skullstrip_orig_vol.in_file_a = anat_image
anat_skullstrip_orig_vol.in_file_b = anat_brain_mask.out_file
rp[R('T1w', desc='skullstrip-afni',
suffix='mask')] = anat_brain_mask.out_file
rp[R('T1w', desc='skullstrip-afni',
suffix='brain')] = anat_skullstrip_orig_vol.out_file
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat = rp[R('T1w', label='reorient')]
anat_skullstrip = NipypeJob(interface=fsl.BET(output_type='NIFTI_GZ',
**config),
reference='anat_skullstrip')
anat_skullstrip.in_file = anat
anat_skullstrip_orig_vol = NipypeJob(
interface=afni.Calc(expr='a*step(b)', outputtype='NIFTI_GZ'),
reference='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.in_file_a = anat
anat_skullstrip_orig_vol.in_file_b = anat_skullstrip.out_file
rp[R('T1w', desc='skullstrip-fsl',
suffix='mask')] = anat_skullstrip.mask_file
rp[R('T1w', desc='skullstrip-fsl',
suffix='brain')] = anat_skullstrip_orig_vol.out_file