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='./'
