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removed SGM and PATH options, added inbuilt masking, voxel size checks
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adsouza
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Oct 14, 2024
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# Copyright (c) 2008-2024 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/. | ||
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import os | ||
import subprocess | ||
from mrtrix3 import MRtrixError | ||
from mrtrix3 import app, path, run | ||
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def usage(base_parser, subparsers): # pylint: disable=unused-variable | ||
parser = subparsers.add_parser('msmt', parents=[base_parser]) | ||
parser.set_author("Arkiev D'Souza ([email protected]) & Robert E. Smith ([email protected])") | ||
parser.set_synopsis('Generate a 5TT image from ODF images.') | ||
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parser.add_argument('odf_wm', type=app.Parser.ImageIn(), help='The input white-matter ODF') | ||
parser.add_argument('odf_gm', type=app.Parser.ImageIn(), help='The input grey-matter ODF') | ||
parser.add_argument('odf_csf', type=app.Parser.ImageIn(), help='The input cerebrospinal fluid ODF') | ||
parser.add_argument('fTT_image', type=app.Parser.ImageOut(), help='The output 5TT image') | ||
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options = parser.add_argument_group('Options specific to the "odf" algorithm') | ||
parser.add_argument('-mask', nargs='?', default=None, type=app.Parser.ImageIn(), help='The input binary brain mask image') | ||
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def execute(): # pylint: disable=unused-variable | ||
# Extract l=0 term from WM | ||
run.command('mrconvert {app.ARGS.odf_wm} -coord 3 0 -axes 0,1,2 wm_vol.mif') | ||
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# check whether the GM and CSF ODF voxel grid match that of wm_vol.mif. If the do not match, regrid with wm_vol.mif as template | ||
command_size_WModf = 'mrinfo -spacing wm_vol.mif' | ||
spacing_size_WModf = subprocess.check_output(command_size_WModf, shell=True).decode('utf-8') | ||
command_size_GModf = 'mrinfo -spacing {app.ARGS.odf_gm}' | ||
spacing_size_GModf = subprocess.check_output(command_size_GModf, shell=True).decode('utf-8') | ||
command_size_CSFodf = 'mrinfo -spacing {app.ARGS.odf_gm}' | ||
spacing_size_CSFodf = subprocess.check_output(command_size_CSFodf, shell=True).decode('utf-8') | ||
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if spacing_size_WModf == spacing_size_GModf: | ||
print("voxel grid of GM and WM ODF match") | ||
run.command('mrconvert {app.ARGS.odf_gm} gm_vol.mif') | ||
else: | ||
print("WARNING: GM ODF has different dimeonsions to WM ODF. Regridding GM ODF") | ||
run.command('mrgrid {app.ARGS.odf_gm} -template wm_vol.mif regrid gm_vol.mif') | ||
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if spacing_size_WModf == spacing_size_CSFodf: | ||
print("voxel grid of CSF and WM ODF match") | ||
run.command('mrconvert {app.ARGS.odf_csf} csf_vol.mif') | ||
else: | ||
print("WARNING: CSF ODF has different dimeonsions to WM ODF. Regridding CSF ODF") | ||
run.command('mrgrid {app.ARGS.odf_csf} -template wm_vol.mif regrid csf_vol.mif') | ||
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# Set negative values to zero | ||
run.command('mrcalc wm_vol.mif 0.0 -max wm_vol_pos.mif') | ||
run.command('mrcalc gm_vol.mif 0.0 -max gm_vol_pos.mif') | ||
run.command('mrcalc csf_vol.mif 0.0 -max csf_vol_pos.mif') | ||
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# Normalize each volume | ||
run.command('mrmath wm_vol_pos.mif gm_vol_pos.mif csf_vol_pos.mif sum totalvol.mif') | ||
run.command('mrcalc wm_vol_pos.mif totalvol.mif -divide wm_vol_pos_norm.mif') | ||
run.command('mrcalc gm_vol_pos.mif totalvol.mif -divide gm_vol_pos_norm.mif') | ||
run.command('mrcalc csf_vol_pos.mif totalvol.mif -divide csf_vol_pos_norm.mif') | ||
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# Create empty volume for SGM and pathology | ||
run.command('mrcalc wm_vol.mif inf -gt empty_vol.mif') | ||
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# Concatenate volumes | ||
run.command('mrcat -datatype float32 gm_vol_pos_norm.mif empty_vol.mif wm_vol_pos_norm.mif csf_vol_pos_norm.mif empty_vol.mif fTT_dirty.mif') | ||
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######################### | ||
# Tidy image by masking # | ||
######################### | ||
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# if mask is provided, use it. If not, create one | ||
if app.ARGS.mask: | ||
# case 1: using provided brainmask | ||
# check if dimensions of brainmask match 5TT_dirty. If not, regrid | ||
command_fTTdirty = 'mrinfo -spacing fTT_dirty.mif' | ||
spacing_fTTdirty = subprocess.check_output(command_fTTdirty, shell=True).decode('utf-8') | ||
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command_mask = 'mrinfo -spacing {app.ARGS.mask}' | ||
spacing_mask = subprocess.check_output(command_mask, shell=True).decode('utf-8') | ||
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if spacing_fTTdirty == spacing_mask: | ||
print("mask has equal dimensions to 5TT image. No regridding of mask required") | ||
run.command('mrcalc fTT_dirty.mif {app.ARGS.mask} -mult result.mif') | ||
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else: | ||
print("WARNING: mask has different dimeonsions to 5TT image. Regridding mask") | ||
run.command('mrgrid {app.ARGS.mask} -template wm_vol.mif regrid - | mrcalc - 0.5 -gt - | mrcalc - fTT_dirty.mif -mult result.mif') | ||
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elif not app.ARGS.mask: | ||
# case 2: Generate a mask that contains only those voxels where the sum of ODF l=0 terms exceeds 0.5/sqrt(4pi); then select the largest component and fill any holes. | ||
# 0.5/sqrt(4pi)=0.1410473959 | ||
run.command('mrcalc totalvol.mif 0.1410473959 -gt - | maskfilter - clean - | maskfilter - fill - | mrcalc - fTT_dirty.mif -mult result.mif') | ||
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run.command(['mrconvert', 'result.mif', app.ARGS.fTT_image], | ||
force=app.FORCE_OVERWRITE, | ||
preserve_pipes=True) | ||
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return 'result.mif' | ||
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