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#!/usr/bin/python3
# Copyright (c) 2008-2025 the MRtrix3 contributors.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Covered Software is provided under this License on an "as is"
# basis, without warranty of any kind, either expressed, implied, or
# statutory, including, without limitation, warranties that the
# Covered Software is free of defects, merchantable, fit for a
# particular purpose or non-infringing.
# See the Mozilla Public License v. 2.0 for more details.
#
# For more details, see http://www.mrtrix.org/.
# note: deal with these warnings properly when we drop support for Python 2:
# pylint: disable=consider-using-f-string
SUPPORTED_OPS = ['mean', 'median', 'sum', 'product', 'rms', 'norm', 'var', 'std', 'min', 'max', 'absmax', 'magmax']
def usage(cmdline): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=no-name-in-module, import-outside-toplevel
cmdline.set_author('Daan Christiaens (daan.christiaens@kcl.ac.uk)')
cmdline.set_synopsis('Apply an mrmath operation to each b-value shell in a DWI series')
cmdline.add_description('The output of this command is a 4D image, where '
'each volume corresponds to a b-value shell (in order of increasing b-value), and '
'the intensities within each volume correspond to the chosen statistic having been computed from across the DWI volumes belonging to that b-value shell.')
cmdline.add_argument('input', help='The input diffusion MRI series')
cmdline.add_argument('operation', choices=SUPPORTED_OPS, help='The operation to be applied to each shell; this must be one of the following: ' + ', '.join(SUPPORTED_OPS))
cmdline.add_argument('output', help='The output image series')
cmdline.add_example_usage('To compute the mean diffusion-weighted signal in each b-value shell',
'dwishellmath dwi.mif mean shellmeans.mif')
app.add_dwgrad_import_options(cmdline)
def execute(): #pylint: disable=unused-variable
from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
from mrtrix3 import app, image, path, run #pylint: disable=no-name-in-module, import-outside-toplevel
# check inputs and outputs
dwi_header = image.Header(path.from_user(app.ARGS.input, False))
if len(dwi_header.size()) != 4:
raise MRtrixError('Input image must be a 4D image')
gradimport = app.read_dwgrad_import_options()
if not gradimport and 'dw_scheme' not in dwi_header.keyval():
raise MRtrixError('No diffusion gradient table provided, and none present in image header')
app.check_output_path(app.ARGS.output)
# import data and gradient table
app.make_scratch_dir()
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' ' + path.to_scratch('in.mif') + gradimport + ' -strides 0,0,0,1')
app.goto_scratch_dir()
# run per-shell operations
files = []
for index, bvalue in enumerate(image.mrinfo('in.mif', 'shell_bvalues').split()):
filename = 'shell-{:02d}.mif'.format(index)
run.command('dwiextract -shells ' + bvalue + ' in.mif - | mrmath -axis 3 - ' + app.ARGS.operation + ' ' + filename)
files.append(filename)
if len(files) > 1:
# concatenate to output file
run.command('mrcat -axis 3 ' + ' '.join(files) + ' out.mif')
run.command('mrconvert out.mif ' + path.from_user(app.ARGS.output), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
else:
# make a 4D image with one volume
app.warn('Only one unique b-value present in DWI data; command mrmath with -axis 3 option may be preferable')
run.command('mrconvert ' + files[0] + ' ' + path.from_user(app.ARGS.output) + ' -axes 0,1,2,-1', mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
# Execute the script
import mrtrix3
mrtrix3.execute() #pylint: disable=no-member
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