def get_inputs(): #pylint: disable=unused-variable
from mrtrix3 import app, path, run
run.command('mrconvert ' + path.from_user(app.ARGS.in_5tt) + ' ' +
path.to_scratch('5tt.mif'))
if app.ARGS.dirs:
run.command('mrconvert ' + path.from_user(app.ARGS.dirs) + ' ' +
path.to_scratch('dirs.mif') + ' -strides 0,0,0,1')
def get_inputs(): #pylint: disable=unused-variable
mask_path = path.to_scratch('mask.mif', False)
if os.path.exists(mask_path):
app.warn('-mask option is ignored by algorithm \'manual\'')
os.remove(mask_path)
run.command('mrconvert ' + path.from_user(app.ARGS.in_voxels) + ' ' + path.to_scratch('in_voxels.mif'))
if app.ARGS.dirs:
run.command('mrconvert ' + path.from_user(app.ARGS.dirs) + ' ' + path.to_scratch('dirs.mif') + ' -strides 0,0,0,1')
def get_inputs(): #pylint: disable=unused-variable
image.check_3d_nonunity(path.from_user(app.ARGS.input, False))
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' ' + path.to_scratch('input.mif'))
if app.ARGS.mask:
run.command('mrconvert ' + path.from_user(app.ARGS.mask) + ' ' + path.to_scratch('mask.mif') + ' -datatype bit -strides -1,+2,+3')
if app.ARGS.t2:
if not image.match(path.from_user(app.ARGS.input, False), path.from_user(app.ARGS.t2, False)):
raise MRtrixError('Provided T2 image does not match input T1 image')
run.command('mrconvert ' + path.from_user(app.ARGS.t2) + ' ' + path.to_scratch('T2.nii') + ' -strides -1,+2,+3')
def check_first(prefix, structures): #pylint: disable=unused-variable
from mrtrix3 import app, path #pylint: disable=import-outside-toplevel
vtk_files = [prefix + '-' + struct + '_first.vtk' for struct in structures]
existing_file_count = sum(
[os.path.exists(filename) for filename in vtk_files])
if existing_file_count != len(vtk_files):
if 'SGE_ROOT' in os.environ and os.environ['SGE_ROOT']:
app.console(
'FSL FIRST job may have been run via SGE; awaiting completion')
app.console(
'(note however that FIRST may fail silently, and hence this script may hang indefinitely)'
)
path.wait_for(vtk_files)
else:
app.DO_CLEANUP = False
raise MRtrixError(
'FSL FIRST has failed; ' +
('only ' if existing_file_count else '') +
str(existing_file_count) + ' of ' + str(len(vtk_files)) +
' structures were segmented successfully (check ' +
path.to_scratch('first.logs', False) + ')')
def get_inputs(): #pylint: disable=unused-variable
check_gif_input(path.from_user(app.ARGS.input, False))
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' ' +
path.to_scratch('input.mif'))
def get_inputs(): #pylint: disable=unused-variable
import shutil
from mrtrix3 import app, path, run
run.command('mrconvert ' + path.from_user(app.ARGS.input) + ' ' + path.to_scratch('input.mif'))
if app.ARGS.lut:
run.function(shutil.copyfile, path.from_user(app.ARGS.lut, False), path.to_scratch('LUT.txt', False))
def get_inputs(): #pylint: disable=unused-variable
# Most freeSurfer files will be accessed in-place; no need to pre-convert them into the temporary directory
# However convert aparc image so that it does not have to be repeatedly uncompressed
run.command('mrconvert ' + path.from_user(os.path.join(app.ARGS.input, 'mri', 'aparc+aseg.mgz'), True) + ' ' + path.to_scratch('aparc.mif', True))
if app.ARGS.template:
run.command('mrconvert ' + path.from_user(app.ARGS.template, True) + ' ' + path.to_scratch('template.mif', True) + ' -axes 0,1,2')