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')