def execute():
import os, sys
from mrtrix3 import app, path, run
lut_input_path = 'LUT.txt'
if not os.path.exists('LUT.txt'):
gif3_home = os.environ.get('GIFDB_HOME', '')
if not gif3_home:
app.error(
'Environment variable GIFDB_HOME is not set. Please set this variable manually, or provide script with path to file GIF3ColourLUT.txt using -lut option.'
)
lut_input_path = os.path.join(gif_home, 'GIF3ColourLUT.txt')
if not os.path.isfile(lut_input_path):
app.error(
'Could not find GIF3 lookup table file (expected location: ' +
lut_input_path + '), and none provided using -lut')
if app.args.sgm_amyg_hipp:
lut_output_file_name = 'GIF32ACT_sgm_amyg_hipp.txt'
else:
lut_output_file_name = 'GIF32ACT.txt'
lut_output_path = os.path.join(path.sharedDataPath(),
path.scriptSubDirName(),
lut_output_file_name)
if not os.path.isfile(lut_output_path):
app.error(
'Could not find lookup table file for converting GIF3 parcellation output to tissues (expected location: '
+ lut_output_path + ')')
# Initial conversion from GIF3 parcellation to five principal tissue types
run.command('labelconvert input.mif ' + lut_input_path + ' ' +
lut_output_path + ' indices.mif')
# Use mrcrop to reduce file size
if app.args.nocrop:
image = 'indices.mif'
else:
image = 'indices_cropped.mif'
run.command(
'mrthreshold indices.mif - -abs 0.5 | mrcrop indices.mif ' +
image + ' -mask -')
# Convert into the 5TT format for ACT
run.command('mrcalc ' + image + ' 1 -eq cgm.mif')
run.command('mrcalc ' + image + ' 2 -eq sgm.mif')
run.command('mrcalc ' + image + ' 3 -eq wm.mif')
run.command('mrcalc ' + image + ' 4 -eq csf.mif')
run.command('mrcalc ' + image + ' 5 -eq path.mif')
run.command(
'mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - result.mif -datatype float32'
)
# Created by Neil Oxtoby on 2018-03-02
# Modified from freesurfer.py in MRtrix3 v3.0
def initialise():
import importlib, pkgutil
from mrtrix3 import app, path
initlist = [ ]
base_parser = app.Parser(description='Base parser for construction of subparsers', parents=[app.cmdline])
subparsers = app.cmdline.add_subparsers(title='Algorithm choices', help='Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ' + ', '.join(getList()), dest='algorithm')
for importer, package_name, ispkg in pkgutil.iter_modules( [ _algorithmsPath() ] ):
module = importlib.import_module('mrtrix3.' + path.scriptSubDirName() + '.' + package_name)
module.initialise(base_parser, subparsers)
initlist.extend(package_name)
app.debug('Initialised algorithms: ' + str(initlist))
def initialise(): #pylint: disable=unused-variable
import importlib, pkgutil
from mrtrix3 import app, path
initlist = [ ]
base_parser = app.Parser(description='Base parser for construction of subparsers', parents=[app.cmdline])
subparsers = app.cmdline.add_subparsers(title='Algorithm choices', help='Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ' + ', '.join(getList()), dest='algorithm')
for dummy_importer, package_name, dummy_ispkg in pkgutil.iter_modules( [ _algorithmsPath() ] ):
module = importlib.import_module('mrtrix3.' + path.scriptSubDirName() + '.' + package_name)
module.initialise(base_parser, subparsers)
initlist.extend(package_name)
app.debug('Initialised algorithms: ' + str(initlist))
def execute():
import os, sys
from mrtrix3 import app, path, run
lut_input_path = 'LUT.txt'
if not os.path.exists('LUT.txt'):
freesurfer_home = os.environ.get('FREESURFER_HOME', '')
if not freesurfer_home:
app.error(
'Environment variable FREESURFER_HOME is not set; please run appropriate FreeSurfer configuration script, set this variable manually, or provide script with path to file FreeSurferColorLUT.txt using -lut option'
)
lut_input_path = os.path.join(freesurfer_home,
'FreeSurferColorLUT.txt')
if not os.path.isfile(lut_input_path):
app.error(
'Could not find FreeSurfer lookup table file (expected location: '
+ freesurfer_lut + '), and none provided using -lut')
if app.args.sgm_amyg_hipp:
lut_output_file_name = 'FreeSurfer2ACT_sgm_amyg_hipp.txt'
else:
lut_output_file_name = 'FreeSurfer2ACT.txt'
lut_output_path = os.path.join(path.sharedDataPath(),
path.scriptSubDirName(),
lut_output_file_name)
if not os.path.isfile(lut_output_path):
app.error(
'Could not find lookup table file for converting FreeSurfer parcellation output to tissues (expected location: '
+ lut_output_path + ')')
# Initial conversion from FreeSurfer parcellation to five principal tissue types
run.command('labelconvert input.mif ' + lut_input_path + ' ' +
lut_output_path + ' indices.mif')
# Use mrcrop to reduce file size
if app.args.nocrop:
image = 'indices.mif'
else:
image = 'indices_cropped.mif'
run.command(
'mrthreshold indices.mif - -abs 0.5 | mrcrop indices.mif ' +
image + ' -mask -')
# Convert into the 5TT format for ACT
run.command('mrcalc ' + image + ' 1 -eq cgm.mif')
run.command('mrcalc ' + image + ' 2 -eq sgm.mif')
run.command('mrcalc ' + image + ' 3 -eq wm.mif')
run.command('mrcalc ' + image + ' 4 -eq csf.mif')
run.command('mrcalc ' + image + ' 5 -eq path.mif')
run.command(
'mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - result.mif -datatype float32'
)
def execute(): #pylint: disable=unused-variable
import os.path #pylint: disable=unused-variable
from mrtrix3 import app, path, run
lut_input_path = 'LUT.txt'
if not os.path.exists('LUT.txt'):
freesurfer_home = os.environ.get('FREESURFER_HOME', '')
if not freesurfer_home:
app.error('Environment variable FREESURFER_HOME is not set; please run appropriate FreeSurfer configuration script, set this variable manually, or provide script with path to file FreeSurferColorLUT.txt using -lut option')
lut_input_path = os.path.join(freesurfer_home, 'FreeSurferColorLUT.txt')
if not os.path.isfile(lut_input_path):
app.error('Could not find FreeSurfer lookup table file (expected location: ' + lut_input_path + '), and none provided using -lut')
if app.args.sgm_amyg_hipp:
lut_output_file_name = 'FreeSurfer2ACT_sgm_amyg_hipp.txt'
else:
lut_output_file_name = 'FreeSurfer2ACT.txt'
lut_output_path = os.path.join(path.sharedDataPath(), path.scriptSubDirName(), lut_output_file_name)
if not os.path.isfile(lut_output_path):
app.error('Could not find lookup table file for converting FreeSurfer parcellation output to tissues (expected location: ' + lut_output_path + ')')
# Initial conversion from FreeSurfer parcellation to five principal tissue types
run.command('labelconvert input.mif ' + lut_input_path + ' ' + lut_output_path + ' indices.mif')
# Use mrcrop to reduce file size
if app.args.nocrop:
image = 'indices.mif'
else:
image = 'indices_cropped.mif'
run.command('mrthreshold indices.mif - -abs 0.5 | mrcrop indices.mif ' + image + ' -mask -')
# Convert into the 5TT format for ACT
run.command('mrcalc ' + image + ' 1 -eq cgm.mif')
run.command('mrcalc ' + image + ' 2 -eq sgm.mif')
run.command('mrcalc ' + image + ' 3 -eq wm.mif')
run.command('mrcalc ' + image + ' 4 -eq csf.mif')
run.command('mrcalc ' + image + ' 5 -eq path.mif')
run.command('mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - result.mif -datatype float32')
def _algorithmsPath(): import os from mrtrix3 import path return os.path.join(os.path.dirname(__file__), path.scriptSubDirName())
def getModule(name): import sys from mrtrix3 import path return sys.modules['mrtrix3.' + path.scriptSubDirName() + '.' + name]
def _algorithmsPath():
import os
from mrtrix3 import path
return os.path.join(os.path.dirname(__file__), path.scriptSubDirName())
def getModule(name):
import sys
from mrtrix3 import path
return sys.modules['mrtrix3.' + path.scriptSubDirName() + '.' + name]
def getModule(name): #pylint: disable=unused-variable import sys from mrtrix3 import path return sys.modules['mrtrix3.' + path.scriptSubDirName() + '.' + name]