def atlas_statistics(file_list, atlas_list):
"""
For each atlas name provided it ƒcalculates for the input image the mean for each region in the atlas and saves it to a TSV file.
:param in_image: A Nifti image
:param in_atlas_list: List of names of atlas to be applied
:return: List of paths to tsv files
"""
from os import getcwd
from os.path import abspath, join
from nipype.utils.filemanip import split_filename
from clinica.utils.atlas import AtlasAbstract
from clinica.utils.statistics import statistics_on_atlas
from clinica.utils.stream import cprint
orig_dir, base, ext = split_filename(file_list)
atlas_classes = AtlasAbstract.__subclasses__()
atlas_statistics_list = []
for atlas in atlas_list:
for atlas_class in atlas_classes:
if atlas_class.get_name_atlas() == atlas:
#out_atlas_statistics = abspath(join(getcwd(), base + '_space-' + atlas + '_map-graymatter_statistics.tsv'))
out_atlas_statistics = abspath(
join('./' + base + '_space-' + atlas +
'_map-graymatter_statistics.tsv'))
cprint(out_atlas_statistics)
statistics_on_atlas(file_list, atlas_class(),
out_atlas_statistics)
atlas_statistics_list.append(out_atlas_statistics)
break
return atlas_statistics_list
def atlas_statistics(in_image, atlas_list):
"""
For each atlas name provided it calculates for the input image the mean for each region in the atlas and saves it to a TSV file.
Args:
in_image: A Nifti image
atlas_list: List of names of atlas to be applied
Returns:
List of paths to TSV files
"""
from os.path import abspath, join
from nipype.utils.filemanip import split_filename
from clinica.utils.atlas import AtlasAbstract
from clinica.utils.statistics import statistics_on_atlas
from clinica.utils.filemanip import get_subject_id
from clinica.utils.ux import print_end_image
subject_id = get_subject_id(in_image)
orig_dir, base, ext = split_filename(in_image)
atlas_classes = AtlasAbstract.__subclasses__()
atlas_statistics_list = []
for atlas in atlas_list:
for atlas_class in atlas_classes:
if atlas_class.get_name_atlas() == atlas:
out_atlas_statistics = abspath(
join('./' + base + '_space-' + atlas +
'_map-graymatter_statistics.tsv'))
statistics_on_atlas(in_image, atlas_class(),
out_atlas_statistics)
atlas_statistics_list.append(out_atlas_statistics)
print_end_image(subject_id)
return atlas_statistics_list
def statistics_on_atlases(in_registered_map, name_map, prefix_file=None):
"""Computes a list of statistics files for each atlas.
Args:
in_registered_map (str): Map already registered on atlases.
name_map (str): Name of the registered map in CAPS format.
prefix_file (Opt[str]):
<prefix_file>_space-<atlas_name>_map-<name_map>_statistics.tsv
Returns:
List of paths leading to the statistics TSV files.
"""
import os
from nipype.utils.filemanip import split_filename
from clinica.utils.atlas import (
AtlasAbstract,
JHUDTI811mm,
JHUTracts01mm,
JHUTracts251mm,
)
from clinica.utils.statistics import statistics_on_atlas
in_atlas_list = [JHUDTI811mm(), JHUTracts01mm(), JHUTracts251mm()]
atlas_statistics_list = []
for atlas in in_atlas_list:
if not isinstance(atlas, AtlasAbstract):
raise TypeError("Atlas element must be an AtlasAbstract type")
if prefix_file is None:
_, base, _ = split_filename(in_registered_map)
filename = (
f"{base}_space-{atlas.get_name_atlas()}"
f"_res-{atlas.get_spatial_resolution()}_map-{name_map}_statistics.tsv"
)
else:
filename = (
f"{prefix_file}_space-{atlas.get_name_atlas()}"
f"_res-{atlas.get_spatial_resolution()}_map-{name_map}_statistics.tsv"
)
out_atlas_statistics = os.path.abspath(
os.path.join(os.getcwd(), filename))
statistics_on_atlas(in_registered_map, atlas, out_atlas_statistics)
atlas_statistics_list.append(out_atlas_statistics)
return atlas_statistics_list
def statistics_on_atlases(in_registered_map, name_map, prefix_file=None):
"""
Computes a list of statistics files for each atlas.
Args:
in_registered_map (str): Map already registered on atlases.
name_map (str): Name of the registered map in CAPS format.
prefix_file (Opt[str]):
<prefix_file>_space-<atlas_name>_map-<name_map>_statistics.tsv
Returns:
List of paths leading to the statistics TSV files.
"""
from os import getcwd
from os.path import abspath, join
from nipype.utils.filemanip import split_filename
from clinica.utils.atlas import (AtlasAbstract, JHUDTI811mm,
JHUTracts01mm, JHUTracts251mm,
JHUTracts501mm)
from clinica.utils.statistics import statistics_on_atlas
# atlas_classes = AtlasAbstract.__subclasses__()
in_atlas_list = [JHUDTI811mm(),
JHUTracts01mm(), JHUTracts251mm()]
atlas_statistics_list = []
for atlas in in_atlas_list:
if not isinstance(atlas, AtlasAbstract):
raise TypeError("Atlas element must be an AtlasAbstract type")
if prefix_file is None:
_, base, _ = split_filename(in_registered_map)
out_atlas_statistics = abspath(
join(getcwd(), '%s_space-%s_res-%s_map-%s_statistics.tsv' %
(base, atlas.get_name_atlas(),
atlas.get_spatial_resolution(), name_map)))
else:
out_atlas_statistics = abspath(
join(getcwd(), '%s_space-%s_res-%s_map-%s_statistics.tsv' %
(prefix_file, atlas.get_name_atlas(),
atlas.get_spatial_resolution(), name_map)))
statistics_on_atlas(in_registered_map, atlas, out_atlas_statistics)
atlas_statistics_list.append(out_atlas_statistics)
return atlas_statistics_list
def atlas_statistics(in_image, in_atlas_list):
"""Generate regional measure from atlas_list in TSV files.
For each atlas name provided it calculates for the input image the mean
for each region in the atlas and saves it to a TSV file.
Args:
in_image: A Nifti image
in_atlas_list: List of names of atlas to be applied
Returns:
List of paths to TSV files
"""
from os import getcwd
from os.path import abspath, join
from nipype.utils.filemanip import split_filename
from clinica.utils.atlas import AtlasAbstract
from clinica.utils.statistics import statistics_on_atlas
orig_dir, base, ext = split_filename(in_image)
atlas_classes = AtlasAbstract.__subclasses__()
atlas_statistics_list = []
for atlas in in_atlas_list:
for atlas_class in atlas_classes:
if atlas_class.get_name_atlas() == atlas:
out_atlas_statistics = abspath(
join(getcwd(),
base + "_space-" + atlas + "_statistics.tsv"))
statistics_on_atlas(in_image, atlas_class(),
out_atlas_statistics)
atlas_statistics_list.append(out_atlas_statistics)
break
return atlas_statistics_list