def write_tsv_files(subjects_dir, subject_id):
"""
Generate statistics TSV files in `subjects_dir`/regional_measures folder for `subject_id`.
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.
write_tsv_files will not be called).
"""
import os
import datetime
from colorama import Fore
from clinica.utils.stream import cprint
from clinica.utils.freesurfer import generate_regional_measures, extract_image_id_from_longitudinal_segmentation
image_id = extract_image_id_from_longitudinal_segmentation(subject_id)
str_image_id = image_id.participant_id + '_' + image_id.session_id + '_' + image_id.long_id
if os.path.isfile(
os.path.join(subjects_dir, subject_id, 'mri', 'aparc+aseg.mgz')):
generate_regional_measures(subjects_dir, subject_id)
else:
now = datetime.datetime.now().strftime('%H:%M:%S')
cprint(
'%s[%s] %s does not contain mri/aseg+aparc.mgz file. '
'Creation of regional_measures/ folder will be skipped.%s' %
(Fore.YELLOW, now, str_image_id.replace('_', ' | '), Fore.RESET))
return subject_id
def write_tsv_files(subjects_dir, image_id):
"""
Generate statistics TSV files in `subjects_dir`/regional_measures folder for `image_id`.
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
write_tsv_files will not be called).
"""
import os
from clinica.utils.freesurfer import generate_regional_measures
from clinica.utils.stream import cprint
if os.path.isfile(
os.path.join(subjects_dir, image_id, "mri", "aparc+aseg.mgz")):
generate_regional_measures(subjects_dir, image_id)
else:
cprint(
msg=
(f"{image_id.replace('_', ' | ')} does not contain "
f"mri/aseg+aparc.mgz file. Creation of regional_measures/ folder will be skipped."
),
lvl="warning",
)
return image_id
def write_tsv_files(subjects_dir, subject_id):
"""Generate statistics TSV files in `subjects_dir`/regional_measures folder for `subject_id`.
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.
write_tsv_files will not be called).
"""
import os
from clinica.utils.freesurfer import (
extract_image_id_from_longitudinal_segmentation,
generate_regional_measures,
)
from clinica.utils.stream import cprint
image_id = extract_image_id_from_longitudinal_segmentation(subject_id)
str_image_id = (image_id.participant_id + "_" + image_id.session_id + "_" +
image_id.long_id)
if os.path.isfile(
os.path.join(subjects_dir, subject_id, "mri", "aparc+aseg.mgz")):
generate_regional_measures(subjects_dir, subject_id)
else:
cprint(
msg=
(f"{str_image_id.replace('_', ' | ')} does not contain mri/aseg+aparc.mgz file. "
"Creation of regional_measures/ folder will be skipped."),
lvl="warning",
)
return subject_id
def write_tsv_files(subjects_dir, image_id):
"""
Generate statistics TSV files in `subjects_dir`/regional_measures folder for `image_id`.
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
write_tsv_files will not be called).
"""
import datetime
import os
from colorama import Fore
from clinica.utils.freesurfer import generate_regional_measures
from clinica.utils.stream import cprint
if os.path.isfile(
os.path.join(subjects_dir, image_id, "mri", "aparc+aseg.mgz")):
generate_regional_measures(subjects_dir, image_id)
else:
now = datetime.datetime.now().strftime("%H:%M:%S")
cprint(
f"{Fore.YELLOW}[{now}] {image_id.replace('_', ' | ')} does not contain "
f"mri/aseg+aparc.mgz file. Creation of regional_measures/ folder will be skipped.{Fore.RESET}"
)
return image_id
def write_tsv_files(subject_id, output_dir):
"""
Generate statistics TSV files for a given subject.
"""
import os
from clinica.utils.freesurfer import generate_regional_measures
participant_id = subject_id.split('_')[0]
session_id = subject_id.split('_')[1]
path_segmentation = os.path.join(os.path.expanduser(output_dir),
'subjects', participant_id, session_id,
't1', 'freesurfer_cross_sectional')
generate_regional_measures(path_segmentation, subject_id)
def write_stats_files(in_subject, in_session, in_symlink_path,
in_longitudinal_result):
"""Generate statistics TSV files for a given {subject,session}.
Statistics are derived from recon-all's own .stats files and are
meant to provide a summary of those.
Args:
in_subject (string): participant_id
in_session (string): session_id
in_symlink_path (string): paths to subject-specific folder
containing all session symlinks for subject_id associated to
in_reconalllong_flags. Used for 1) retrieving the path to
recon-all generated .tsv files 2) write stats files in a
subfolder of the folder containing the symlink to
{subject,session}
in_longitudinal_result (Boolean): Used to force longitudinal
recon-all to be run before generating the .tsv files from
the longitudinal processing
Returns:
out_stats_path (string): path to the folder containing
all the .tsv stats files for {subject,session}
"""
import os
from clinica.utils.freesurfer import generate_regional_measures
# get path to longitudinal folder in working dir (where recon-all
# results are stored, including .stats files)
seg_path = os.path.expanduser(in_symlink_path)
# define output dir for the .tsv files
subses_long_id = '{0}_{1}.long.{0}'.format(in_subject, in_session)
subses_long_stats_subdir = "{0}_stats".format(subses_long_id)
out_stats_path = os.path.join(seg_path, subses_long_stats_subdir)
# generate the .tsv files from .stats files
subses_id = '{0}_{1}'.format(in_subject, in_session)
generate_regional_measures(seg_path,
subses_id,
output_dir=out_stats_path,
longitudinal=True)
return out_stats_path