def test_registration_via_synth(): from registration_via_synth import ( create_linear_func_to_synth, create_linear_rho_to_anat, create_bbr_func_to_anat_via_synth, ) import nipype.pipeline.engine as pe import nipype.interfaces.fsl as fsl import nipype.interfaces.utility as util func_file = "/sam/wave1/sub3120/rest_1/lfo.nii.gz" anat_skull_file = "/sam/wave1/sub3120/anat_1/head.nii.gz" anat_bet_file = "/sam/wave1/sub3120/anat_1/brain.nii.gz" mni_brain_file = "/frodo/shared/fsl5/data/standard/MNI152_T1_2mm_brain.nii.gz" mni_skull_file = "/frodo/shared/fsl5/data/standard/MNI152_T1_2mm.nii.gz" synth_file = "/sam/wave1/sub3120/calib_1/cal_synth.nii.gz" cal_bo_file = "/sam/wave1/sub3120/calib_1/cal_reg_boRPI.nii.gz" cal_rho_file = "/sam/wave1/sub3120/calib_1/cal_rho.nii.gz" wm_seg = "/sam/wave1/sub3120/anat_1/brain_wmseg.nii.gz" bbr_sched = "/frodo/shared/fsl5/etc/flirtsch/bbr.sch" # nr1 = create_linear_func_to_synth() # nr1.inputs.inputspec.func = func_file # nr1.inputs.inputspec.synth = synth_file # nr1.inputs.inputspec.calib_bo_RPI = cal_bo_file # # nr1.base_dir = './' # nr1.run() # nr2 = create_linear_rho_to_anat() # nr2.inputs.inputspec.anat_skull = anat_skull_file # nr2.inputs.inputspec.calib_rho = cal_rho_file # # nr2.base_dir = './' # nr2.run() # nr3 = create_bbr_func_to_anat_via_synth() nr3.inputs.inputspec.func = func_file nr3.inputs.inputspec.synth = synth_file nr3.inputs.inputspec.calib_bo_RPI = cal_bo_file nr3.inputs.inputspec.anat_skull = anat_skull_file nr3.inputs.inputspec.calib_rho = cal_rho_file nr3.inputs.inputspec.anat_wm_segmentation = wm_seg nr3.inputs.inputspec.bbr_schedule = bbr_sched nr3.base_dir = "./" nr3.run()
calib_preproc = create_calib_preproc() calib_preproc.inputs.inputspec.bo_name = '/sam/wave1/sub4974/calib_1/cal_bo.nii.gz' calib_preproc.inputs.inputspec.rho_name = '/sam/wave1/sub4974/calib_1/cal_rho.nii.gz' calib_preproc.inputs.inputspec.rs_name = '/sam/wave1/sub4974/calib_1/cal_rs.nii.gz' calib_preproc.inputs.inputspec.reg_bo_name = '/sam/wave1/sub4974/calib_1/cal_reg_bo.nii.gz' preproc = create_func_preproc(slice_timing_correction=True) preproc.inputs.inputspec.start_idx = 4 preproc.inputs.inputspec.stop_idx = 180 preproc.inputs.inputspec.rest = func_file preproc.inputs.scan_params.tr = '2.0' preproc.inputs.scan_params.ref_slice = 1 preproc.inputs.scan_params.acquisition = 'alt+z' nr3 = create_bbr_func_to_anat_via_synth() nr3.inputs.inputspec.func = func_file nr3.inputs.inputspec.anat_skull = anat_skull_file nr3.inputs.inputspec.anat_wm_segmentation = wm_seg nr3.inputs.inputspec.bbr_schedule = bbr_sched B0_workflow.connect(calib_preproc, 'outputspec.cal_reg_bo_RPI', preproc, 'inputspec.calib_reg_bo_RPI') B0_workflow.connect(calib_preproc, 'outputspec.cal_synth_RPI', nr3, 'inputspec.synth_RPI') B0_workflow.connect(calib_preproc, 'outputspec.cal_bo_RPI', nr3, 'inputspec.calib_bo_RPI') B0_workflow.connect(calib_preproc, 'outputspec.cal_rho_RPI', nr3, 'inputspec.calib_rho_RPI') B0_workflow.base_dir = './'
calib_preproc.inputs.inputspec.rs_name='/sam/wave1/sub4974/calib_1/cal_rs.nii.gz' calib_preproc.inputs.inputspec.reg_bo_name='/sam/wave1/sub4974/calib_1/cal_reg_bo.nii.gz' preproc = create_func_preproc(slice_timing_correction=True) preproc.inputs.inputspec.start_idx = 4 preproc.inputs.inputspec.stop_idx = 180 preproc.inputs.inputspec.rest=func_file preproc.inputs.scan_params.tr = '2.0' preproc.inputs.scan_params.ref_slice = 1 preproc.inputs.scan_params.acquisition = 'alt+z' nr3 = create_bbr_func_to_anat_via_synth() nr3.inputs.inputspec.func = func_file nr3.inputs.inputspec.anat_skull = anat_skull_file nr3.inputs.inputspec.anat_wm_segmentation=wm_seg nr3.inputs.inputspec.bbr_schedule=bbr_sched B0_workflow.connect(calib_preproc, 'outputspec.cal_reg_bo_RPI',preproc, 'inputspec.calib_reg_bo_RPI' ) B0_workflow.connect(calib_preproc, 'outputspec.cal_synth_RPI',nr3, 'inputspec.synth_RPI' ) B0_workflow.connect(calib_preproc, 'outputspec.cal_bo_RPI',nr3, 'inputspec.calib_bo_RPI' ) B0_workflow.connect(calib_preproc, 'outputspec.cal_rho_RPI',nr3, 'inputspec.calib_rho_RPI' ) B0_workflow.base_dir='./'