def test_ApplyWarp_outputs():
output_map = dict(out_file=dict(), )
outputs = ApplyWarp.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_ApplyWarp_inputs():
input_map = dict(
abswarp=dict(argstr="--abs", xor=["relwarp"]),
args=dict(argstr="%s"),
datatype=dict(argstr="--datatype=%s"),
environ=dict(nohash=True, usedefault=True),
field_file=dict(argstr="--warp=%s"),
ignore_exception=dict(nohash=True, usedefault=True),
in_file=dict(argstr="--in=%s", mandatory=True, position=0),
interp=dict(argstr="--interp=%s", position=-2),
mask_file=dict(argstr="--mask=%s"),
out_file=dict(argstr="--out=%s", genfile=True, hash_files=False, position=2),
output_type=dict(),
postmat=dict(argstr="--postmat=%s"),
premat=dict(argstr="--premat=%s"),
ref_file=dict(argstr="--ref=%s", mandatory=True, position=1),
relwarp=dict(argstr="--rel", position=-1, xor=["abswarp"]),
superlevel=dict(argstr="--superlevel=%s"),
supersample=dict(argstr="--super"),
terminal_output=dict(mandatory=True, nohash=True),
)
inputs = ApplyWarp.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_ApplyWarp_outputs():
output_map = dict(out_file=dict())
outputs = ApplyWarp.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_ApplyWarp_inputs():
input_map = dict(abswarp=dict(argstr='--abs',
xor=['relwarp'],
),
args=dict(argstr='%s',
),
datatype=dict(argstr='--datatype=%s',
),
environ=dict(nohash=True,
usedefault=True,
),
field_file=dict(argstr='--warp=%s',
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
in_file=dict(argstr='--in=%s',
mandatory=True,
position=0,
),
interp=dict(argstr='--interp=%s',
position=-2,
),
mask_file=dict(argstr='--mask=%s',
),
out_file=dict(argstr='--out=%s',
genfile=True,
hash_files=False,
position=2,
),
output_type=dict(),
postmat=dict(argstr='--postmat=%s',
),
premat=dict(argstr='--premat=%s',
),
ref_file=dict(argstr='--ref=%s',
mandatory=True,
position=1,
),
relwarp=dict(argstr='--rel',
position=-1,
xor=['abswarp'],
),
superlevel=dict(argstr='--superlevel=%s',
),
supersample=dict(argstr='--super',
),
terminal_output=dict(mandatory=True,
nohash=True,
),
)
inputs = ApplyWarp.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
# extract first volume
fslroi = ExtractROI()
fslroi.inputs.in_file = file_in[i]
fslroi.inputs.roi_file = file_vol0
fslroi.inputs.output_type = "NIFTI"
fslroi.inputs.t_min = 0
fslroi.inputs.t_size = 1
fslroi.run()
# exexute gnl correction
gnl_correction(file_vol0, file_bash, file_coeff, python3_env, python2_env,
path_file, False)
# apply warp to first volume
applywarp = ApplyWarp()
applywarp.inputs.in_file = file_in[i]
applywarp.inputs.ref_file = file_in[i]
applywarp.inputs.relwarp = True
applywarp.inputs.field_file = os.path.join(path_file, "grad",
"warp.nii.gz")
applywarp.inputs.output_type = "NIFTI"
applywarp.inputs.out_file = file_out
applywarp.inputs.interp = "spline"
applywarp.run()
# normalise warped output image to initial intensity range
data_img = nb.load(file_in[i])
data_array = data_img.get_fdata()
max_data = np.max(data_array)
min_data = np.min(data_array)
def gnl_correction(input,
file_bash,
file_coeff,
python3_env,
python2_env,
path_output,
cleanup=True):
"""
The purpose of the following function is to correct for gradient nonlinearities. A corrected
file is written using spline interpolation. The function needs FSL to be included in the search
path.
Inputs:
*input: filename of input image.
*file_bash: filename of bash script which calls the gradient unwarping toolbox.
*file_coeff: filename of siemens coefficient file.
*python3_env: name of python3 virtual environment.
*python2_env: name of python2 virtual environment.
*path_output: path where output is written.
*cleanup: delete intermediate files.
created by Daniel Haenelt
Date created: 10-01-2020
Last modified: 10-01-2020
"""
import os
import shutil as sh
import numpy as np
import nibabel as nb
from nipype.interfaces.fsl import ConvertWarp, Merge
from nipype.interfaces.fsl.maths import MeanImage
from nipype.interfaces.fsl.preprocess import ApplyWarp
from lib.io.get_filename import get_filename
from lib.cmap.generate_coordinate_mapping import generate_coordinate_mapping
# get fileparts
path, name, ext = get_filename(input)
# make subfolders
path_grad = os.path.join(path_output, "grad")
if not os.path.exists(path_grad):
os.makedirs(path_grad)
# parse arguments
file_output = os.path.join(path_output, name + "_gnlcorr" + ext)
file_warp = os.path.join(path_grad, "warp.nii.gz")
file_jacobian = os.path.join(path_grad, "warp_jacobian.nii.gz")
# run gradient unwarp
os.system("bash " + file_bash + \
" " + python3_env + \
" " + python2_env + \
" " + path_grad + \
" " + input + \
" trilinear.nii.gz" + \
" " + file_coeff)
# now create an appropriate warpfield output (relative convention)
convertwarp = ConvertWarp()
convertwarp.inputs.reference = os.path.join(path_grad, "trilinear.nii.gz")
convertwarp.inputs.warp1 = os.path.join(path_grad, "fullWarp_abs.nii.gz")
convertwarp.inputs.abswarp = True
convertwarp.inputs.out_relwarp = True
convertwarp.inputs.out_file = file_warp
convertwarp.inputs.args = "--jacobian=" + file_jacobian
convertwarp.run()
# convertwarp's jacobian output has 8 frames, each combination of one-sided differences, so average them
calcmean = MeanImage()
calcmean.inputs.in_file = file_jacobian
calcmean.inputs.dimension = "T"
calcmean.inputs.out_file = file_jacobian
calcmean.run()
# apply warp to first volume
applywarp = ApplyWarp()
applywarp.inputs.in_file = input
applywarp.inputs.ref_file = input
applywarp.inputs.relwarp = True
applywarp.inputs.field_file = file_warp
applywarp.inputs.output_type = "NIFTI"
applywarp.inputs.out_file = file_output
applywarp.inputs.interp = "spline"
applywarp.run()
# normalise warped output image to initial intensity range
data_img = nb.load(input)
data_array = data_img.get_fdata()
max_data = np.max(data_array)
min_data = np.min(data_array)
data_img = nb.load(file_output)
data_array = data_img.get_fdata()
data_array[data_array < min_data] = 0
data_array[data_array > max_data] = max_data
output = nb.Nifti1Image(data_array, data_img.affine, data_img.header)
nb.save(output, file_output)
# calculate gradient deviations
os.system("calc_grad_perc_dev" + \
" --fullwarp=" + file_warp + \
" -o " + os.path.join(path_grad,"grad_dev"))
# merge directions
merger = Merge()
merger.inputs.in_files = [
os.path.join(path_grad, "grad_dev_x.nii.gz"),
os.path.join(path_grad, "grad_dev_y.nii.gz"),
os.path.join(path_grad, "grad_dev_z.nii.gz")
]
merger.inputs.dimension = 't'
merger.inputs.merged_file = os.path.join(path_grad, "grad_dev.nii.gz")
merger.run()
# convert from % deviation to absolute
data_img = nb.load(os.path.join(path_grad, "grad_dev.nii.gz"))
data_array = data_img.get_fdata()
data_array = data_array / 100
output = nb.Nifti1Image(data_array, data_img.affine, data_img.header)
nb.save(output, os.path.join(path_grad, "grad_dev.nii.gz"))
# warp coordinate mapping
generate_coordinate_mapping(input,
0,
path_grad,
suffix="gnl",
time=False,
write_output=True)
applywarp = ApplyWarp()
applywarp.inputs.in_file = os.path.join(path_grad, "cmap_gnl.nii")
applywarp.inputs.ref_file = input
applywarp.inputs.relwarp = True
applywarp.inputs.field_file = file_warp
applywarp.inputs.out_file = os.path.join(path_grad, "cmap_gnl.nii")
applywarp.inputs.interp = "trilinear"
applywarp.inputs.output_type = "NIFTI"
applywarp.run()
# clean intermediate files
if cleanup:
sh.rmtree(path_grad, ignore_errors=True)