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 execute(): #pylint: disable=unused-variable
class Input(object):
def __init__(self, filename, prefix, mask_filename=''):
self.filename = filename
self.prefix = prefix
self.mask_filename = mask_filename
input_dir = path.from_user(app.ARGS.input_dir, False)
if not os.path.exists(input_dir):
raise MRtrixError('input directory not found')
in_files = path.all_in_dir(input_dir, dir_path=False)
if len(in_files) <= 1:
raise MRtrixError(
'not enough images found in input directory: more than one image is needed to perform a group-wise intensity normalisation'
)
app.console('performing global intensity normalisation on ' +
str(len(in_files)) + ' input images')
mask_dir = path.from_user(app.ARGS.mask_dir, False)
if not os.path.exists(mask_dir):
raise MRtrixError('mask directory not found')
mask_files = path.all_in_dir(mask_dir, dir_path=False)
if len(mask_files) != len(in_files):
raise MRtrixError(
'the number of images in the mask directory does not equal the number of images in the input directory'
)
mask_common_postfix = os.path.commonprefix([i[::-1]
for i in mask_files])[::-1]
mask_prefixes = []
for mask_file in mask_files:
mask_prefixes.append(mask_file.split(mask_common_postfix)[0])
common_postfix = os.path.commonprefix([i[::-1] for i in in_files])[::-1]
input_list = []
for i in in_files:
subj_prefix = i.split(common_postfix)[0]
if subj_prefix not in mask_prefixes:
raise MRtrixError(
'no matching mask image was found for input image ' + i)
image.check_3d_nonunity(os.path.join(input_dir, i))
index = mask_prefixes.index(subj_prefix)
input_list.append(Input(i, subj_prefix, mask_files[index]))
app.make_scratch_dir()
app.goto_scratch_dir()
path.make_dir('fa')
progress = app.ProgressBar('Computing FA images', len(input_list))
for i in input_list:
run.command('dwi2tensor ' +
path.quote(os.path.join(input_dir, i.filename)) +
' -mask ' +
path.quote(os.path.join(mask_dir, i.mask_filename)) +
' - | tensor2metric - -fa ' +
os.path.join('fa', i.prefix + '.mif'))
progress.increment()
progress.done()
app.console('Generating FA population template')
run.command('population_template fa fa_template.mif' + ' -mask_dir ' +
mask_dir + ' -type rigid_affine_nonlinear' +
' -rigid_scale 0.25,0.5,0.8,1.0' +
' -affine_scale 0.7,0.8,1.0,1.0' +
' -nl_scale 0.5,0.75,1.0,1.0,1.0' + ' -nl_niter 5,5,5,5,5' +
' -warp_dir warps' + ' -linear_no_pause' +
' -scratch population_template' +
('' if app.DO_CLEANUP else ' -nocleanup'))
app.console('Generating WM mask in template space')
run.command('mrthreshold fa_template.mif -abs ' + app.ARGS.fa_threshold +
' template_wm_mask.mif')
progress = app.ProgressBar('Intensity normalising subject images',
len(input_list))
path.make_dir(path.from_user(app.ARGS.output_dir, False))
path.make_dir('wm_mask_warped')
for i in input_list:
run.command(
'mrtransform template_wm_mask.mif -interp nearest -warp_full ' +
os.path.join('warps', i.prefix + '.mif') + ' ' +
os.path.join('wm_mask_warped', i.prefix + '.mif') +
' -from 2 -template ' + os.path.join('fa', i.prefix + '.mif'))
run.command('dwinormalise individual ' +
path.quote(os.path.join(input_dir, i.filename)) + ' ' +
os.path.join('wm_mask_warped', i.prefix + '.mif') +
' temp.mif')
run.command(
'mrconvert temp.mif ' +
path.from_user(os.path.join(app.ARGS.output_dir, i.filename)),
mrconvert_keyval=path.from_user(
os.path.join(input_dir, i.filename), False),
force=app.FORCE_OVERWRITE)
os.remove('temp.mif')
progress.increment()
progress.done()
app.console('Exporting template images to user locations')
run.command('mrconvert template_wm_mask.mif ' +
path.from_user(app.ARGS.wm_mask),
mrconvert_keyval='NULL',
force=app.FORCE_OVERWRITE)
run.command('mrconvert fa_template.mif ' +
path.from_user(app.ARGS.fa_template),
mrconvert_keyval='NULL',
force=app.FORCE_OVERWRITE)