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 print_end_pipeline(t1w, final_file):
"""
Display end message for <subject_id> when <final_file> is connected.
"""
from clinica.utils.ux import print_end_image
from clinica.utils.filemanip import get_subject_id
print_end_image(get_subject_id(t1w))
def save_to_caps(source_dir, caps_dir, overwrite_caps, pipeline_parameters):
"""Save `source_dir`/ to CAPS folder.
This function copies outputs of `source_dir`/ to
`caps_dir`/groups/<group_id>/<statistics>/surfstat_<glm_type>/
The `source_dir`/ folder should contain the following elements:
- group-<group_label>_<group_1_or_2>-lt-<group_1_or_2>_measure-<measure>_fwhm-<label>_suffix.ext
or
- group-<group_label>_correlation-<label>_contrast-{-|+}_measure-<measure>_fwhm-<label>_suffix.ext
and
- group-<group_label>_covariates.tsv
- group-<group_label>_glm.json
Raise:
NotImplementedError: If overwrite_caps=True.
"""
import os
import shutil
from clinica.utils.ux import print_end_image
group_id = "group-" + pipeline_parameters["group_label"]
if pipeline_parameters["glm_type"] == "group_comparison":
surfstat_folder = "surfstat_" + pipeline_parameters["glm_type"]
elif pipeline_parameters["glm_type"] == "correlation":
surfstat_folder = "surfstat_" + pipeline_parameters[
"glm_type"] + "_analysis"
else:
raise NotImplementedError(
"The other GLM situations have not been implemented in this pipeline."
)
destination_dir = os.path.join(os.path.expanduser(caps_dir), "groups",
group_id, "statistics", surfstat_folder)
if overwrite_caps:
raise NotImplementedError(
"save_to_caps(overwrite_caps=True) not implemented")
shutil.copytree(source_dir, destination_dir, symlinks=True)
print_end_image(group_id)
def print_end_pipeline(in_bids_or_caps_file: str, final_file: str) -> None:
from clinica.utils.filemanip import get_subject_id
from clinica.utils.ux import print_end_image
print_end_image(get_subject_id(in_bids_or_caps_file))
def print_end_pipeline(image_id, final_file):
"""Display end message for `image_id` when `final_file` is connected."""
from clinica.utils.ux import print_end_image
print_end_image(image_id)
def save_to_caps(source_dir, image_id, caps_dir, overwrite_caps=False):
"""Save `source_dir`/`image_id`/ to CAPS folder.
This function copies outputs of `source_dir`/`image_id`/ to
`caps_dir`/subjects/<participant_id>/<session_id>/t1_freesurfer_cross_sectional/
where `image_id` = <participant_id>_<session_id>.
The `source_dir`/`image_id`/ folder should contain the following elements:
- fsaverage, lh.EC_average and rh.EC_average symbolic links
- `image_id`/ folder containing the FreeSurfer segmentation
- regional_measures/ folder containing TSV files
Notes:
We do not need to check the line "finished without error" in scripts/recon-all.log.
If an error occurs, it will be detected by Nipype and the next nodes (including
save_to_caps will not be called).
Raise:
FileNotFoundError: If symbolic links in `source_dir`/`image_id` folder are not removed
IOError: If the `source_dir`/`image_id` folder does not contain FreeSurfer segmentation.
"""
import os
import datetime
import errno
import shutil
from colorama import Fore
from clinica.utils.stream import cprint
from clinica.utils.ux import print_end_image
participant_id = image_id.split('_')[0]
session_id = image_id.split('_')[1]
destination_dir = os.path.join(os.path.expanduser(caps_dir), 'subjects',
participant_id, session_id, 't1',
'freesurfer_cross_sectional')
representative_file = os.path.join(image_id, 'mri', 'aparc+aseg.mgz')
representative_source_file = os.path.join(os.path.expanduser(source_dir),
image_id, representative_file)
representative_destination_file = os.path.join(destination_dir,
representative_file)
if os.path.isfile(representative_source_file):
# Remove symbolic links before the copy
try:
os.unlink(
os.path.join(os.path.expanduser(source_dir), image_id,
'fsaverage'))
os.unlink(
os.path.join(os.path.expanduser(source_dir), image_id,
'lh.EC_average'))
os.unlink(
os.path.join(os.path.expanduser(source_dir), image_id,
'rh.EC_average'))
except FileNotFoundError as e:
if e.errno != errno.ENOENT:
raise e
if os.path.isfile(representative_destination_file):
if overwrite_caps:
shutil.rmtree(destination_dir)
shutil.copytree(os.path.join(source_dir, image_id),
destination_dir,
symlinks=True)
print_end_image(image_id)
else:
now = datetime.datetime.now().strftime('%H:%M:%S')
cprint('%s[%s] %s does not contain mri/aseg+aparc.mgz file. '
'Copy will be skipped.%s' %
(Fore.YELLOW, now, image_id.replace('_', ' | '), Fore.RESET))
return image_id
def print_end_pipeline(subject_id, final_file):
"""Display end message for <subject_id> when <final_file> is connected."""
from clinica.utils.ux import print_end_image
print_end_image(subject_id)
def save_to_caps(source_dir,
image_id,
list_session_ids,
caps_dir,
overwrite_caps=False):
"""Save `source_dir`/`image_id`/ to CAPS folder.
This function copies FreeSurfer segmentation and regional_measures folder of `source_dir`/`image_id`/ to
`caps_dir`/subjects/<participant_id>/<long_id>/freesurfer_unbiased_template/
where `image_id` = <participant_id>_<long_id>.
The `source_dir`/`image_id`/ folder should contain the following elements:
- fsaverage, lh.EC_average and rh.EC_average symbolic links automatically generated by recon-all
- symbolic links to cross-sectional segmentation(s) and unbiased template needed for recon-all
- <participant_id>_<long_id>/ folder containing the FreeSurfer segmentation
Notes:
We do not need to check the line "finished without error" in scripts/recon-all.log.
If an error occurs, it will be detected by Nipype and the next nodes (i.e. save_to_caps will not be called).
"""
import os
import datetime
import shutil
from colorama import Fore
from clinica.utils.stream import cprint
from clinica.utils.longitudinal import save_long_id
from clinica.utils.ux import print_end_image
participant_id = image_id.split('_')[0]
long_id = image_id.split('_')[1]
destination_dir = os.path.join(os.path.expanduser(caps_dir), 'subjects',
participant_id, long_id,
'freesurfer_unbiased_template')
# Save <long_id>_sessions.tsv to retrieve sessions used to generate <long_id>
sessions_tsv_path = os.path.join(os.path.expanduser(caps_dir), 'subjects',
participant_id, long_id)
if not os.path.isfile(
os.path.join(sessions_tsv_path, long_id + '_sessions.tsv')):
save_long_id(list_session_ids, sessions_tsv_path,
long_id + '_sessions.tsv')
# Save FreeSurfer segmentation
representative_file = os.path.join(image_id, 'mri', 'aparc+aseg.mgz')
representative_source_file = os.path.join(os.path.expanduser(source_dir),
image_id, representative_file)
representative_destination_file = os.path.join(destination_dir,
representative_file)
if os.path.isfile(representative_source_file):
if os.path.isfile(representative_destination_file):
if overwrite_caps:
shutil.rmtree(destination_dir)
shutil.copytree(src=os.path.join(source_dir, image_id,
image_id),
dst=os.path.join(destination_dir, image_id),
symlinks=True)
else:
shutil.copytree(src=os.path.join(source_dir, image_id, image_id),
dst=os.path.join(destination_dir, image_id),
symlinks=True)
print_end_image(image_id)
else:
now = datetime.datetime.now().strftime('%H:%M:%S')
cprint(
'%s[%s] %s does not contain mri/aseg+aparc.mgz file. Copy will be skipped.%s'
% (Fore.YELLOW, now, image_id.replace('_', ' | '), Fore.RESET))
return image_id
def save_to_caps(source_dir, image_id, caps_dir, overwrite_caps=False):
"""Save `source_dir`/`image_id`/ to CAPS folder.
This function copies FreeSurfer segmentation and regional_measures folder of `source_dir`/`image_id`/ to
`caps_dir`/subjects/<participant_id>/<session_id>/t1_freesurfer_cross_sectional/
where `image_id` = <participant_id>_<session_id>.
The `source_dir`/`image_id`/ folder should contain the following elements:
- fsaverage, lh.EC_average and rh.EC_average symbolic links automatically generated by recon-all
- `image_id`/ folder containing the FreeSurfer segmentation
- regional_measures/ folder containing TSV files
Notes:
We do not need to check the line "finished without error" in scripts/recon-all.log.
If an error occurs, it will be detected by Nipype and the next nodes (i.e. save_to_caps will not be called).
"""
import os
import shutil
from clinica.utils.stream import cprint
from clinica.utils.ux import print_end_image
participant_id = image_id.split("_")[0]
session_id = image_id.split("_")[1]
destination_dir = os.path.join(
os.path.expanduser(caps_dir),
"subjects",
participant_id,
session_id,
"t1",
"freesurfer_cross_sectional",
)
# Save FreeSurfer segmentation
representative_file = os.path.join(image_id, "mri", "aparc+aseg.mgz")
representative_source_file = os.path.join(os.path.expanduser(source_dir),
image_id, representative_file)
representative_destination_file = os.path.join(destination_dir,
representative_file)
if os.path.isfile(representative_source_file):
if os.path.isfile(representative_destination_file):
if overwrite_caps:
shutil.rmtree(destination_dir)
shutil.copytree(
src=os.path.join(source_dir, image_id, image_id),
dst=os.path.join(destination_dir, image_id),
symlinks=True,
)
shutil.copytree(
src=os.path.join(source_dir, image_id,
"regional_measures"),
dst=os.path.join(destination_dir, "regional_measures"),
symlinks=True,
)
else:
shutil.copytree(
src=os.path.join(source_dir, image_id, image_id),
dst=os.path.join(destination_dir, image_id),
symlinks=True,
)
shutil.copytree(
src=os.path.join(source_dir, image_id, "regional_measures"),
dst=os.path.join(destination_dir, "regional_measures"),
symlinks=True,
)
print_end_image(image_id)
else:
cprint(
msg=
f"{image_id.replace('_', ' | ')} does not contain mri/aseg+aparc.mgz file. Copy will be skipped.",
lvl="warning",
)
return image_id
def save_to_caps(source_dir, subject_id, caps_dir, overwrite_caps=False):
"""Save `source_dir`/`subject_id`/ to CAPS folder.
This function copies FreeSurfer segmentation and regional_measures folder of `source_dir`/`image_id`/ to
`caps_dir`/subjects/<participant_id>/<session_id>/<long_id>/t1_freesurfer_longitudinal/
where `image_id` = <participant_id>_<session_id>_<long_id>.
The `source_dir`/`image_id`/ folder should contain the following elements:
- fsaverage, lh.EC_average and rh.EC_average symbolic links automatically generated by recon-all
- symbolic links to cross-sectional segmentation(s) and unbiased template needed for recon-all
- <participant_id>_<session_id>.long.<participant_id>_<long_id>/ folder containing the FreeSurfer segmentation
- regional_measures/ folder containing TSV files
Notes:
We do not need to check the line "finished without error" in scripts/recon-all.log.
If an error occurs, it will be detected by Nipype and the next nodes (i.e. save_to_caps will not be called).
"""
import datetime
import os
import shutil
from colorama import Fore
from clinica.utils.freesurfer import extract_image_id_from_longitudinal_segmentation
from clinica.utils.stream import cprint
from clinica.utils.ux import print_end_image
image_id = extract_image_id_from_longitudinal_segmentation(subject_id)
participant_id = image_id.participant_id
session_id = image_id.session_id
long_id = image_id.long_id
str_image_id = (image_id.participant_id + "_" + image_id.session_id + "_" +
image_id.long_id)
destination_dir = os.path.join(
os.path.expanduser(caps_dir),
"subjects",
participant_id,
session_id,
"t1",
long_id,
"freesurfer_longitudinal",
)
# Save FreeSurfer segmentation
representative_file = os.path.join(subject_id, "mri", "aparc+aseg.mgz")
representative_source_file = os.path.join(os.path.expanduser(source_dir),
str_image_id,
representative_file)
representative_destination_file = os.path.join(destination_dir,
representative_file)
if os.path.isfile(representative_source_file):
if os.path.isfile(representative_destination_file):
if overwrite_caps:
shutil.rmtree(destination_dir)
shutil.copytree(
src=os.path.join(source_dir, subject_id, subject_id),
dst=os.path.join(destination_dir, subject_id),
symlinks=True,
)
shutil.copytree(
src=os.path.join(source_dir, subject_id,
"regional_measures"),
dst=os.path.join(destination_dir, "regional_measures"),
symlinks=True,
)
else:
shutil.copytree(
src=os.path.join(source_dir, str_image_id, subject_id),
dst=os.path.join(destination_dir, subject_id),
symlinks=True,
)
shutil.copytree(
src=os.path.join(source_dir, str_image_id,
"regional_measures"),
dst=os.path.join(destination_dir, "regional_measures"),
symlinks=True,
)
print_end_image(str_image_id)
else:
now = datetime.datetime.now().strftime("%H:%M:%S")
cprint(
f"{Fore.YELLOW}[{now}] {subject_id.replace('_', ' | ')} does not contain "
f"mri/aseg+aparc.mgz file. Copy will be skipped.{Fore.RESET}")
return str_image_id
