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