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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/.
# Script for estimating response functions for spherical deconvolution
# A number of different approaches are available within this script for performing response function estimation.
def usage(cmdline): #pylint: disable=unused-variable
from mrtrix3 import algorithm, app #pylint: disable=no-name-in-module, import-outside-toplevel
cmdline.set_author('Robert E. Smith (robert.smith@florey.edu.au) and Thijs Dhollander (thijs.dhollander@gmail.com)')
cmdline.set_synopsis('Estimate response function(s) for spherical deconvolution')
cmdline.add_description('dwi2response offers different algorithms for performing various types of response function estimation. The name of the algorithm must appear as the first argument on the command-line after \'dwi2response\'. The subsequent arguments and options depend on the particular algorithm being invoked.')
cmdline.add_description('Each algorithm available has its own help page, including necessary references; e.g. to see the help page of the \'fa\' algorithm, type \'dwi2response fa\'.')
# General options
common_options = cmdline.add_argument_group('General dwi2response options')
common_options.add_argument('-mask', help='Provide an initial mask for response voxel selection')
common_options.add_argument('-voxels', help='Output an image showing the final voxel selection(s)')
common_options.add_argument('-shells', help='The b-value(s) to use in response function estimation (comma-separated list in case of multiple b-values, b=0 must be included explicitly)')
common_options.add_argument('-lmax', help='The maximum harmonic degree(s) for response function estimation (comma-separated list in case of multiple b-values)')
app.add_dwgrad_import_options(cmdline)
# Import the command-line settings for all algorithms found in the relevant directory
algorithm.usage(cmdline)
def execute(): #pylint: disable=unused-variable
from mrtrix3 import MRtrixError #pylint: disable=no-name-in-module, import-outside-toplevel
from mrtrix3 import algorithm, app, image, path, run #pylint: disable=no-name-in-module, import-outside-toplevel
# Find out which algorithm the user has requested
alg = algorithm.get_module(app.ARGS.algorithm)
# Check for prior existence of output files, and grab any input files, used by the particular algorithm
if app.ARGS.voxels:
app.check_output_path(app.ARGS.voxels)
alg.check_output_paths()
# Sanitise some inputs, and get ready for data import
if app.ARGS.lmax:
try:
lmax = [ int(x) for x in app.ARGS.lmax.split(',') ]
if any(lmax_value%2 for lmax_value in lmax):
raise MRtrixError('Value of lmax must be even')
except:
raise MRtrixError('Parameter lmax must be a number')
if alg.needs_single_shell() and not len(lmax) == 1:
raise MRtrixError('Can only specify a single lmax value for single-shell algorithms')
shells_option = ''
if app.ARGS.shells:
try:
shells_values = [ int(round(float(x))) for x in app.ARGS.shells.split(',') ]
except:
raise MRtrixError('-shells option should provide a comma-separated list of b-values')
if alg.needs_single_shell() and not len(shells_values) == 1:
raise MRtrixError('Can only specify a single b-value shell for single-shell algorithms')
shells_option = ' -shells ' + app.ARGS.shells
singleshell_option = ''
if alg.needs_single_shell():
singleshell_option = ' -singleshell -no_bzero'
grad_import_option = app.read_dwgrad_import_options()
if not grad_import_option and 'dw_scheme' not in image.Header(path.from_user(app.ARGS.input, False)).keyval():
raise MRtrixError('Script requires diffusion gradient table: either in image header, or using -grad / -fslgrad option')
app.make_scratch_dir()
# Get standard input data into the scratch directory
if alg.needs_single_shell() or shells_option:
app.console('Importing DWI data (' + path.from_user(app.ARGS.input) + ') and selecting b-values...')
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' - -strides 0,0,0,1' + grad_import_option + ' | dwiextract - ' + path.to_scratch('dwi.mif') + shells_option + singleshell_option, show=False)
else: # Don't discard b=0 in multi-shell algorithms
app.console('Importing DWI data (' + path.from_user(app.ARGS.input) + ')...')
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' ' + path.to_scratch('dwi.mif') + ' -strides 0,0,0,1' + grad_import_option, show=False)
if app.ARGS.mask:
app.console('Importing mask (' + path.from_user(app.ARGS.mask) + ')...')
run.command('mrconvert ' + path.from_user(app.ARGS.mask) + ' ' + path.to_scratch('mask.mif') + ' -datatype bit', show=False)
alg.get_inputs()
app.goto_scratch_dir()
if alg.supports_mask():
if app.ARGS.mask:
# Check that the brain mask is appropriate
mask_header = image.Header('mask.mif')
if mask_header.size()[:3] != image.Header('dwi.mif').size()[:3]:
raise MRtrixError('Dimensions of provided mask image do not match DWI')
if not (len(mask_header.size()) == 3 or (len(mask_header.size()) == 4 and mask_header.size()[3] == 1)):
raise MRtrixError('Provided mask image needs to be a 3D image')
else:
app.console('Computing brain mask (dwi2mask)...')
run.command('dwi2mask dwi.mif mask.mif', show=False)
if not image.statistics('mask.mif', mask='mask.mif').count:
raise MRtrixError(('Provided' if app.ARGS.mask else 'Generated') + ' mask image does not contain any voxels')
# From here, the script splits depending on what estimation algorithm is being used
alg.execute()
# Execute the script
import mrtrix3
mrtrix3.execute() #pylint: disable=no-member
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