# Copyright (C) 2009-2022, Ecole Polytechnique Federale de Lausanne (EPFL) and
# Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, and CMP3 contributors
# All rights reserved.
#
# This software is distributed under the open-source license Modified BSD.
"""Definition of classes and functions for handling non-GUI general events."""
# General imports
import multiprocessing
import fnmatch
import sys
import os
import warnings
from traits.api import *
from bids import BIDSLayout
# Own imports
from cmp.pipelines.anatomical import anatomical as Anatomical_pipeline
from cmp.pipelines.diffusion import diffusion as Diffusion_pipeline
from cmp.pipelines.functional import fMRI as FMRI_pipeline
from cmtklib.config import (
anat_load_config_json,
anat_save_config,
dmri_load_config_json,
dmri_save_config,
fmri_load_config_json,
fmri_save_config,
)
from cmtklib.bids.io import (
__cmp_directory__,
__nipype_directory__,
__freesurfer_directory__
)
from cmtklib.bids.utils import write_derivative_description
# Ignore some warnings
warnings.filterwarnings(
"ignore",
message="UserWarning: No valid root directory found for domain 'derivatives'."
" Falling back on the Layout's root directory. If this isn't the intended behavior, "
"make sure the config file for this domain includes a 'root' key.",
)
[docs]class ProjectInfo(HasTraits):
"""Class used to store all properties of a processing project.
Attributes
-----------
base_directory: traits.Directory
BIDS dataset root directory
output_directory: traits.Directory
Output directory
bids_layout : bids.BIDSLayout
Instance of pybids `BIDSLayout`
subjects : traits.List
List of subjects in the dataset
subject :
Subject being processed
in the form ``sub-XX``
subject_sessions : traits.List
List of sessions for the subject being processed
subject_session : trait.Str
Session of the subject being processed
in the form ``ses-YY``
diffusion_imaging_model : traits.Str
Diffusion imaging model that can be
'DSI', 'DTI', 'HARDI' or 'multishell'
dmri_bids_acqs : traits.List
List diffusion imaging models extracted from ``acq-<label>`` filename part.
dmri_bids_acq :
Diffusion imaging model being processed
anat_runs : traits.List
List of run labels for T1w scans with multiple runs
anat_run : traits.Str
Run being processed for T1w scans with multiple runs
dmri_runs : traits.List
List of run labels for DWI scans with multiple runs
dmri_run : traits.Str
Run being processed for DWI scans with multiple runs
fmri_runs : traits.List
List of run labels for fMRI scans with multiple runs
fmri_run : traits.Str
Run being processed for fMRI scans with multiple runs
parcellation_scheme : traits.Str
Parcellation scheme used
(Default: 'Lausanne2018')
atlas_info : traits.Dict
Dictionary storing parcellation atlas information
See :class:`~cmp.parcellation.parcellation.ParcellationStage` for more details
freesurfer_subjects_dir : traits.Str
Freesurfer subjects directory
freesurfer_subject_id : traits.Str
Freesurfer subject ID
t1_available : Bool
True if T1w scans were found
(Default: False)
dmri_available : Bool
True if DWI scans were found
(Default: False)
fmri_available : Bool
True if fMRI scans were found
(Default: False)
anat_config_error_msg : traits.Str
Error message for the anatomical pipeline configuration file
anat_config_to_load : traits.Str
Path to a configuration file for the anatomical pipeline
anat_available_config : traits.List
List of configuration files for the anatomical pipeline
anat_stage_names : traits.List
List of anatomical pipeline stage names
anat_custom_last_stage : traits.Str
Custom last anatomical pipeline stage to be processed
dmri_config_error_msg : traits.Str
Error message for the diffusion pipeline configuration file
dmri_config_to_load : traits.Str
Path to a configuration file for the diffusion pipeline
dmri_available_config : traits.List
List of configuration files for the anatomical pipeline
dmri_stage_names : traits.List
List of diffusion pipeline stage names
dmri_custom_last_stage : traits.Str
Custom last diffusion pipeline stage to be processed
fmri_config_error_msg : traits.Str
Error message for the fMRI pipeline configuration file
fmri_config_to_load : traits.Str
Path to a configuration file for the fMRI pipeline
fmri_available_config : traits.List
List of configuration files for the fMRI pipeline
fmri_stage_names : traits.List
List of fMRI pipeline stage names
fmri_custom_last_stage : traits.Str
Custom last fMRI pipeline stage to be processed
number_of_cores : int
Number of cores used by Nipype workflow execution engine
to distribute independent processing nodes
(Must be in the range of your local resources)
"""
base_directory = Directory
output_directory = Directory
bids_layout = Instance(BIDSLayout)
subjects = List([])
subject = Enum(values="subjects")
number_of_subjects = Int()
subject_sessions = List([])
subject_session = Enum(values="subject_sessions")
anat_warning_msg = Str(
"\nWarning: selected directory is already configured for anatomical data processing.\n\n"
"Do you want to reset the configuration to default parameters ?\n"
)
dmri_warning_msg = Str(
"\nWarning: selected directory is already configured for diffusion data processing.\n\n"
"Do you want to reset the configuration to default parameters ?\n"
)
fmri_warning_msg = Str(
"\nWarning: selected directory is already configured for resting-state data processing.\n\n"
"Do you want to reset the configuration to default parameters ?\n"
)
# process_type = Enum('diffusion',['diffusion','fMRI'])
diffusion_imaging_model = Enum("DTI", ["DSI", "DTI", "HARDI", "multishell"])
parcellation_scheme = Str("Lausanne2018")
atlas_info = Dict()
freesurfer_subjects_dir = Str("")
freesurfer_subject_id = Str("")
pipeline_processing_summary = List()
t1_available = Bool(False)
dmri_available = Bool(False)
fmri_available = Bool(False)
anat_config_error_msg = Str("")
anat_config_to_load = Str()
anat_available_config = List()
anat_config_to_load_msg = Str(
"Several configuration files available. Select which one to load:\n"
)
anat_last_date_processed = Str("Not yet processed")
anat_last_stage_processed = Str("Not yet processed")
anat_stage_names = List
anat_custom_last_stage = Str
dmri_config_error_msg = Str("")
dmri_config_to_load = Str()
dmri_available_config = List()
dmri_config_to_load_msg = Str(
"Several configuration files available. Select which one to load:\n"
)
dmri_last_date_processed = Str("Not yet processed")
dmri_last_stage_processed = Str("Not yet processed")
dmri_stage_names = List
dmri_custom_last_stage = Str
fmri_config_error_msg = Str("")
fmri_config_to_load = Str()
fmri_available_config = List()
fmri_config_to_load_msg = Str(
"Several configuration files available. Select which one to load:\n"
)
fmri_last_date_processed = Str("Not yet processed")
fmri_last_stage_processed = Str("Not yet processed")
fmri_stage_names = List
fmri_custom_last_stage = Str
number_of_cores = Enum(1, list(range(1, multiprocessing.cpu_count() + 1)))
[docs]def refresh_folder(
bids_directory, derivatives_directory, subject, input_folders, session=None
):
"""Creates (if needed) the folder hierarchy.
Parameters
----------
bids_directory : os.path
BIDS dataset root directory
derivatives_directory : os.path
Output (derivatives) directory
subject : string
BIDS subject label (``sub-XX``)
input_folders : List of string
List of folder to be created in ``derivatives_directory``/'cmp-<version>'/``subject``
session : string
BIDS session label (``ses-YY``)
"""
paths = []
if session is None or session == "":
paths.append(os.path.join(derivatives_directory, __freesurfer_directory__, subject))
paths.append(os.path.join(derivatives_directory, __cmp_directory__, subject))
paths.append(os.path.join(derivatives_directory, __nipype_directory__, subject))
for in_f in input_folders:
paths.append(os.path.join(derivatives_directory, __cmp_directory__, subject, in_f))
# paths.append(os.path.join(derivatives_directory,'nipype',subject,in_f))
else:
paths.append(
os.path.join(
derivatives_directory, __freesurfer_directory__, "%s_%s" % (subject, session)
)
)
paths.append(os.path.join(derivatives_directory, __cmp_directory__, subject, session))
paths.append(os.path.join(derivatives_directory, __nipype_directory__, subject, session))
for in_f in input_folders:
paths.append(
os.path.join(derivatives_directory, __cmp_directory__, subject, session, in_f)
)
# paths.append(os.path.join(derivatives_directory,'nipype',subject,session,in_f))
for full_p in paths:
if not os.path.exists(full_p):
try:
os.makedirs(full_p)
except os.error:
print("%s was already existing" % full_p)
finally:
print("Created directory %s" % full_p)
write_derivative_description(bids_directory, derivatives_directory, __cmp_directory__)
write_derivative_description(bids_directory, derivatives_directory, __freesurfer_directory__)
write_derivative_description(bids_directory, derivatives_directory, __nipype_directory__)
[docs]def init_dmri_project(project_info, bids_layout, is_new_project, gui=True, debug=False):
"""Initialize the diffusion processing pipeline.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of ``cmp.project.CMP_Project_Info`` object
bids_layout : bids.BIDSLayout
Instance of ``BIDSLayout`` object
is_new_project : bool
Specify if it corresponds or not to a new project.
If `True`, it will create initial pipeline configuration files.
gui : bool
Might be obsolete and removed in future versions
debug : bool
If `True`, display extra prints to support debugging
Returns
-------
dmri_pipeline : Instance(cmp.pipelines.diffusion.diffusion.DiffusionPipeline)
`DiffusionPipeline` object instance
"""
dmri_pipeline = Diffusion_pipeline.DiffusionPipeline(project_info)
bids_directory = os.path.abspath(project_info.base_directory)
derivatives_directory = os.path.abspath(project_info.output_directory)
if len(project_info.subject_sessions) > 0:
refresh_folder(
bids_directory,
derivatives_directory,
project_info.subject,
dmri_pipeline.input_folders,
session=project_info.subject_session,
)
else:
refresh_folder(
bids_directory,
derivatives_directory,
project_info.subject,
dmri_pipeline.input_folders,
)
dmri_inputs_checked = dmri_pipeline.check_input(layout=bids_layout, gui=gui)
if dmri_inputs_checked:
if (
is_new_project and dmri_pipeline is not None
): # and dmri_pipelineis not None:
print("> Initialize dmri project")
if not os.path.exists(derivatives_directory):
try:
os.makedirs(derivatives_directory)
except os.error:
print("... Info : %s was already existing" % derivatives_directory)
finally:
print("... Info : Created directory %s" % derivatives_directory)
if (project_info.subject_session != "") and (
project_info.subject_session is not None
):
project_info.dmri_config_file = os.path.join(
derivatives_directory,
"%s_%s_diffusion_config.ini"
% (project_info.subject, project_info.subject_session),
)
else:
project_info.dmri_config_file = os.path.join(
derivatives_directory,
"%s_diffusion_config.ini" % project_info.subject,
)
if os.path.exists(project_info.dmri_config_file):
warn_res = project_info.configure_traits(view="dmri_warning_view")
if warn_res:
print(
"... Read : Diffusion config file (%s)"
% project_info.dmri_config_file
)
dmri_save_config(dmri_pipeline, project_info.dmri_config_file)
else:
return None
else:
print(
"... Create : Diffusion config file (%s)"
% project_info.dmri_config_file
)
dmri_save_config(dmri_pipeline, project_info.dmri_config_file)
else:
if debug:
print("int_project dmri_pipeline.global_config.subjects : ")
print(dmri_pipeline.global_conf.subjects)
dmri_conf_loaded = dmri_load_config_json(
dmri_pipeline, project_info.dmri_config_file
)
if not dmri_conf_loaded:
return None
dmri_pipeline.config_file = project_info.dmri_config_file
else:
print("INFO: Missing diffusion inputs")
return dmri_inputs_checked, dmri_pipeline
[docs]def init_fmri_project(project_info, bids_layout, is_new_project, gui=True, debug=False):
"""Initialize the fMRI processing pipeline.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of ``cmp.project.CMP_Project_Info`` object
bids_layout : bids.BIDSLayout
Instance of ``BIDSLayout`` object
is_new_project : bool
Specify if it corresponds or not to a new project.
If `True`, it will create initial pipeline configuration files.
gui : bool
Might be obsolete and removed in future versions
debug : bool
If `True`, display extra prints to support debugging
Returns
-------
fmri_pipeline : Instance(cmp.pipelines.functional.fMRI.fMRIPipeline)
`fMRIPipeline` object instance
"""
fmri_pipeline = FMRI_pipeline.fMRIPipeline(project_info)
bids_directory = os.path.abspath(project_info.base_directory)
derivatives_directory = os.path.abspath(project_info.output_directory)
if len(project_info.subject_sessions) > 0:
refresh_folder(
bids_directory,
derivatives_directory,
project_info.subject,
fmri_pipeline.input_folders,
session=project_info.subject_session,
)
else:
refresh_folder(
bids_directory,
derivatives_directory,
project_info.subject,
fmri_pipeline.input_folders,
)
fmri_inputs_checked = fmri_pipeline.check_input(layout=bids_layout, gui=gui)
if fmri_inputs_checked:
if (
is_new_project and fmri_pipeline is not None
): # and fmri_pipelineis not None:
print("> Initialize fmri project")
if not os.path.exists(derivatives_directory):
try:
os.makedirs(derivatives_directory)
except os.error:
print("... Info : %s was already existing" % derivatives_directory)
finally:
print("... Info : Created directory %s" % derivatives_directory)
if (project_info.subject_session != "") and (
project_info.subject_session is not None
):
project_info.fmri_config_file = os.path.join(
derivatives_directory,
"%s_%s_fMRI_config.ini"
% (project_info.subject, project_info.subject_session),
)
else:
project_info.fmri_config_file = os.path.join(
derivatives_directory, "%s_fMRI_config.ini" % project_info.subject
)
if os.path.exists(project_info.fmri_config_file):
warn_res = project_info.configure_traits(view="fmri_warning_view")
if warn_res:
print(
"... Read : fMRI config file (%s)"
% project_info.fmri_config_file
)
fmri_load_config_json(fmri_pipeline, project_info.fmri_config_file)
else:
return None
else:
print(
"... Create : fMRI config file (%s)" % project_info.fmri_config_file
)
fmri_save_config(fmri_pipeline, project_info.fmri_config_file)
else:
if debug:
print("int_project fmri_pipeline.global_config.subjects : ")
print(fmri_pipeline.global_conf.subjects)
fmri_conf_loaded = fmri_load_config_json(
fmri_pipeline, project_info.fmri_config_file
)
if not fmri_conf_loaded:
return None
fmri_pipeline.config_file = project_info.fmri_config_file
else:
print("INFO : Missing fmri inputs")
return fmri_inputs_checked, fmri_pipeline
[docs]def init_anat_project(project_info, is_new_project, debug=False):
"""Initialize the anatomical processing pipeline.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of ``cmp.project.CMP_Project_Info`` object
is_new_project : bool
Specify if it corresponds or not to a new project.
If `True`, it will create initial pipeline configuration files.
debug : bool
If `True`, display extra prints to support debugging
Returns
-------
anat_pipeline : Instance(cmp.pipelines.anatomical.anatomical.AnatomicalPipeline)
`AnatomicalPipeline` object instance
"""
anat_pipeline = Anatomical_pipeline.AnatomicalPipeline(project_info)
bids_directory = os.path.abspath(project_info.base_directory)
derivatives_directory = os.path.abspath(project_info.output_directory)
if (project_info.subject_session != "") and (
project_info.subject_session is not None
):
if debug:
print("Refresh folder WITH session")
refresh_folder(
bids_directory,
derivatives_directory,
project_info.subject,
anat_pipeline.input_folders,
session=project_info.subject_session,
)
else:
if debug:
print("Refresh folder WITHOUT session")
refresh_folder(
bids_directory,
derivatives_directory,
project_info.subject,
anat_pipeline.input_folders,
)
if is_new_project and anat_pipeline is not None: # and dmri_pipelineis not None:
print("> Initialize anatomical project")
if not os.path.exists(derivatives_directory):
try:
os.makedirs(derivatives_directory)
except os.error:
print("... Info: %s was already existing" % derivatives_directory)
finally:
print("... Info : Created directory %s" % derivatives_directory)
if (project_info.subject_session != "") and (
project_info.subject_session is not None
):
project_info.anat_config_file = os.path.join(
derivatives_directory,
"%s_%s_anatomical_config.ini"
% (project_info.subject, project_info.subject_session),
)
else:
project_info.anat_config_file = os.path.join(
derivatives_directory, "%s_anatomical_config.ini" % project_info.subject
)
if os.path.exists(project_info.anat_config_file):
warn_res = project_info.configure_traits(view="anat_warning_view")
if warn_res:
anat_save_config(anat_pipeline, project_info.anat_config_file)
else:
return None
else:
anat_save_config(anat_pipeline, project_info.anat_config_file)
else:
if debug:
print("int_project anat_pipeline.global_config.subjects : ")
print(anat_pipeline.global_conf.subjects)
anat_conf_loaded = anat_load_config_json(
anat_pipeline, project_info.anat_config_file
)
if not anat_conf_loaded:
return None
anat_pipeline.config_file = project_info.anat_config_file
return anat_pipeline
[docs]def update_anat_last_processed(project_info, pipeline):
"""Update last processing information of a :class:`~cmp.pipelines.anatomical.anatomical.AnatomicalPipeline`.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of `CMP_Project_Info` object
pipeline : cmp.pipelines.anatomical.anatomical.AnatomicalPipeline
Instance of `AnatomicalPipeline` object
"""
# last date
if os.path.exists(
os.path.join(project_info.output_directory, __nipype_directory__, project_info.subject)
):
# out_dirs = os.listdir(os.path.join(
# project_info.output_directory, 'nipype', project_info.subject))
# for out in out_dirs:
# if (project_info.last_date_processed == "Not yet processed" or
# out > project_info.last_date_processed):
# pipeline.last_date_processed = out
# project_info.last_date_processed = out
if (
project_info.anat_last_date_processed == "Not yet processed"
or pipeline.now > project_info.anat_last_date_processed
):
pipeline.anat_last_date_processed = pipeline.now
project_info.anat_last_date_processed = pipeline.now
# last stage
if os.path.exists(
os.path.join(
project_info.output_directory,
__nipype_directory__,
project_info.subject,
"anatomical_pipeline",
)
):
stage_dirs = []
for _, dirnames, _ in os.walk(
os.path.join(
project_info.output_directory,
__nipype_directory__,
project_info.subject,
"anatomical_pipeline",
)
):
for dirname in fnmatch.filter(dirnames, "*_stage"):
stage_dirs.append(dirname)
for stage in pipeline.ordered_stage_list:
if stage.lower() + "_stage" in stage_dirs:
pipeline.last_stage_processed = stage
project_info.anat_last_stage_processed = stage
# last parcellation scheme
project_info.parcellation_scheme = pipeline.parcellation_scheme
project_info.atlas_info = pipeline.atlas_info
[docs]def update_dmri_last_processed(project_info, pipeline):
"""Update last processing information of an :class:`~cmp.pipelines.diffusion.diffusion.DiffusionPipeline`.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of `CMP_Project_Info` object
pipeline : cmp.pipelines.diffusion.diffusion.DiffusionPipeline
Instance of `DiffusionPipeline` object
"""
# last date
if os.path.exists(
os.path.join(project_info.output_directory, __nipype_directory__, project_info.subject)
):
# out_dirs = os.listdir(os.path.join(
# project_info.output_directory, 'nipype', project_info.subject))
# for out in out_dirs:
# if (project_info.last_date_processed == "Not yet processed" or
# out > project_info.last_date_processed):
# pipeline.last_date_processed = out
# project_info.last_date_processed = out
if (
project_info.dmri_last_date_processed == "Not yet processed"
or pipeline.now > project_info.dmri_last_date_processed
):
pipeline.dmri_last_date_processed = pipeline.now
project_info.dmri_last_date_processed = pipeline.now
# last stage
if os.path.exists(
os.path.join(
project_info.output_directory,
__nipype_directory__,
project_info.subject,
"diffusion_pipeline",
)
):
stage_dirs = []
for _, dirnames, _ in os.walk(
os.path.join(
project_info.output_directory,
__nipype_directory__,
project_info.subject,
"diffusion_pipeline",
)
):
for dirname in fnmatch.filter(dirnames, "*_stage"):
stage_dirs.append(dirname)
for stage in pipeline.ordered_stage_list:
if stage.lower() + "_stage" in stage_dirs:
pipeline.last_stage_processed = stage
project_info.dmri_last_stage_processed = stage
[docs]def update_fmri_last_processed(project_info, pipeline):
"""Update last processing information of an :class:`~cmp.pipelines.functional.fMRI.fMRIPipeline`.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of `CMP_Project_Info` object
pipeline : cmp.pipelines.functional.fMRI.fMRIPipeline
Instance of `fMRIPipeline` object
"""
# last date
if os.path.exists(
os.path.join(project_info.output_directory, __nipype_directory__, project_info.subject)
):
# out_dirs = os.listdir(os.path.join(
# project_info.output_directory, 'nipype', project_info.subject))
# for out in out_dirs:
# if (project_info.last_date_processed == "Not yet processed" or
# out > project_info.last_date_processed):
# pipeline.last_date_processed = out
# project_info.last_date_processed = out
if (
project_info.fmri_last_date_processed == "Not yet processed"
or pipeline.now > project_info.fmri_last_date_processed
):
pipeline.fmri_last_date_processed = pipeline.now
project_info.fmri_last_date_processed = pipeline.now
# last stage
if os.path.exists(
os.path.join(
project_info.output_directory,
__nipype_directory__,
project_info.subject,
"fMRI_pipeline",
)
):
stage_dirs = []
for _, dirnames, _ in os.walk(
os.path.join(
project_info.output_directory,
__nipype_directory__,
project_info.subject,
"fMRI_pipeline",
)
):
for dirname in fnmatch.filter(dirnames, "*_stage"):
stage_dirs.append(dirname)
for stage in pipeline.ordered_stage_list:
if stage.lower() + "_stage" in stage_dirs:
pipeline.last_stage_processed = stage
project_info.dmri_last_stage_processed = stage
[docs]def run_individual(
bids_dir,
output_dir,
participant_label,
session_label,
anat_pipeline_config,
dwi_pipeline_config,
func_pipeline_config,
number_of_threads=1,
):
"""Function that creates the processing pipeline for complete coverage.
Parameters
----------
bids_dir : string
BIDS dataset root directory
output_dir : string
Output (derivatives) directory
participant_label : string
BIDS participant / subject label (``sub-XX``)
session_label : string
BIDS session label (``ses-XX``)
anat_pipeline_config : string
Path to anatomical pipeline configuration file
dwi_pipeline_config : string
Path to diffusion pipeline configuration file
func_pipeline_config : string
Path to fMRI pipeline configuration file
number_of_threads : int
Number of threads used by programs relying on the OpenMP library
"""
project = ProjectInfo()
project.base_directory = os.path.abspath(bids_dir)
project.output_directory = os.path.abspath(output_dir)
project.subjects = ["{}".format(participant_label)]
project.subject = "{}".format(participant_label)
try:
bids_layout = BIDSLayout(project.base_directory)
except Exception:
print("Exception : Raised at BIDSLayout")
sys.exit(1)
if session_label is not None:
project.subject_sessions = ["{}".format(session_label)]
project.subject_session = "{}".format(session_label)
print("INFO : Detected session(s)")
else:
print("INFO : No detected session")
project.subject_sessions = [""]
project.subject_session = ""
project.anat_config_file = os.path.abspath(anat_pipeline_config)
# Perform only the anatomical pipeline
if dwi_pipeline_config is None and func_pipeline_config is None:
anat_pipeline = init_anat_project(project, False)
if anat_pipeline is not None:
anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
print(f"--- Set Freesurfer and ANTs to use {number_of_threads} threads by the means of OpenMP")
anat_pipeline.stages["Segmentation"].config.number_of_threads = number_of_threads
if anat_valid_inputs:
print(">> Process anatomical pipeline")
anat_pipeline.process()
else:
print("ERROR : Invalid inputs")
sys.exit(1)
anat_pipeline.check_stages_execution()
anat_pipeline.fill_stages_outputs()
# Perform the anatomical and the diffusion pipelines
elif dwi_pipeline_config is not None and func_pipeline_config is None:
project.dmri_config_file = os.path.abspath(dwi_pipeline_config)
anat_pipeline = init_anat_project(project, False)
if anat_pipeline is not None:
anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
print(f"--- Set Freesurfer and ANTs to use {number_of_threads} threads by the means of OpenMP")
anat_pipeline.stages[ "Segmentation"].config.number_of_threads = number_of_threads
if anat_valid_inputs:
print(">> Process anatomical pipeline")
anat_pipeline.process()
else:
print("ERROR : Invalid inputs")
sys.exit(1)
anat_valid_outputs, msg = anat_pipeline.check_output()
anat_pipeline.check_stages_execution()
anat_pipeline.fill_stages_outputs()
project.freesurfer_subjects_dir = anat_pipeline.stages["Segmentation"].config.freesurfer_subjects_dir
project.freesurfer_subject_id = anat_pipeline.stages["Segmentation"].config.freesurfer_subject_id
if anat_valid_outputs:
dmri_valid_inputs, dmri_pipeline = init_dmri_project(
project, bids_layout, False
)
if dmri_pipeline is not None:
dmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
dmri_pipeline.atlas_info = anat_pipeline.atlas_info
if anat_pipeline.parcellation_scheme == "Custom":
dmri_pipeline.custom_atlas_name = anat_pipeline.stages["Parcellation"].config.custom_parcellation.atlas
dmri_pipeline.custom_atlas_res = anat_pipeline.stages["Parcellation"].config.custom_parcellation.res
if dmri_valid_inputs:
dmri_pipeline.process()
else:
print(" ... ERROR : Invalid inputs")
sys.exit(1)
dmri_pipeline.check_stages_execution()
dmri_pipeline.fill_stages_outputs()
else:
print(msg)
sys.exit(1)
# Perform the anatomical and the fMRI pipelines
elif dwi_pipeline_config is None and func_pipeline_config is not None:
project.fmri_config_file = os.path.abspath(func_pipeline_config)
anat_pipeline = init_anat_project(project, False)
if anat_pipeline is not None:
anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
print(f"--- Set Freesurfer and ANTs to use {number_of_threads} threads by the means of OpenMP")
anat_pipeline.stages[ "Segmentation"].config.number_of_threads = number_of_threads
if anat_valid_inputs:
print(">> Process anatomical pipeline")
anat_pipeline.process()
else:
print("ERROR : Invalid inputs")
sys.exit(1)
anat_valid_outputs, msg = anat_pipeline.check_output()
anat_pipeline.check_stages_execution()
anat_pipeline.fill_stages_outputs()
project.freesurfer_subjects_dir = anat_pipeline.stages["Segmentation"].config.freesurfer_subjects_dir
project.freesurfer_subject_id = anat_pipeline.stages["Segmentation"].config.freesurfer_subject_id
if anat_valid_outputs:
fmri_valid_inputs, fmri_pipeline = init_fmri_project(
project, bids_layout, False
)
if fmri_pipeline is not None:
fmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
fmri_pipeline.atlas_info = anat_pipeline.atlas_info
if anat_pipeline.parcellation_scheme == "Custom":
fmri_pipeline.custom_atlas_name = anat_pipeline.stages["Parcellation"].config.custom_parcellation.atlas
fmri_pipeline.custom_atlas_res = anat_pipeline.stages["Parcellation"].config.custom_parcellation.res
if fmri_valid_inputs:
print(">> Process fmri pipeline")
fmri_pipeline.process()
else:
print(" ... ERROR : Invalid inputs")
sys.exit(1)
fmri_pipeline.check_stages_execution()
fmri_pipeline.fill_stages_outputs()
else:
print(msg)
sys.exit(1)
# Perform all pipelines (anatomical/diffusion/fMRI)
elif dwi_pipeline_config is not None and func_pipeline_config is not None:
project.dmri_config_file = os.path.abspath(dwi_pipeline_config)
project.fmri_config_file = os.path.abspath(func_pipeline_config)
anat_pipeline = init_anat_project(project, False)
if anat_pipeline is not None:
anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
print(f"--- Set Freesurfer and ANTs to use {number_of_threads} threads by the means of OpenMP")
anat_pipeline.stages[ "Segmentation"].config.number_of_threads = number_of_threads
if anat_valid_inputs:
print(">> Process anatomical pipeline")
anat_pipeline.process()
else:
print(" ... ERROR : Invalid inputs")
sys.exit(1)
anat_valid_outputs, msg = anat_pipeline.check_output()
anat_pipeline.check_stages_execution()
anat_pipeline.fill_stages_outputs()
project.freesurfer_subjects_dir = anat_pipeline.stages["Segmentation"].config.freesurfer_subjects_dir
project.freesurfer_subject_id = anat_pipeline.stages["Segmentation"].config.freesurfer_subject_id
if anat_valid_outputs:
dmri_valid_inputs, dmri_pipeline = init_dmri_project(
project, bids_layout, False
)
if dmri_pipeline is not None:
dmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
dmri_pipeline.atlas_info = anat_pipeline.atlas_info
if anat_pipeline.parcellation_scheme == "Custom":
dmri_pipeline.custom_atlas_name = anat_pipeline.stages["Parcellation"].config.custom_parcellation.atlas
dmri_pipeline.custom_atlas_res = anat_pipeline.stages["Parcellation"].config.custom_parcellation.res
if dmri_valid_inputs:
print(">> Process diffusion pipeline")
dmri_pipeline.process()
else:
print(" ... ERROR : Invalid inputs")
sys.exit(1)
dmri_pipeline.check_stages_execution()
dmri_pipeline.fill_stages_outputs()
fmri_valid_inputs, fmri_pipeline = init_fmri_project(
project, bids_layout, False
)
if fmri_pipeline is not None:
fmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
fmri_pipeline.atlas_info = anat_pipeline.atlas_info
fmri_pipeline.subjects_dir = anat_pipeline.stages["Segmentation"].config.freesurfer_subjects_dir
fmri_pipeline.subject_id = anat_pipeline.stages[ "Segmentation"].config.freesurfer_subject_id
if anat_pipeline.parcellation_scheme == "Custom":
fmri_pipeline.custom_atlas_name = anat_pipeline.stages["Parcellation"].config.custom_parcellation.atlas
fmri_pipeline.custom_atlas_res = anat_pipeline.stages["Parcellation"].config.custom_parcellation.res
print("Freesurfer subjects dir: {}".format(fmri_pipeline.subjects_dir))
print("Freesurfer subject id: {}".format(fmri_pipeline.subject_id))
# print sys.argv[offset+9]
if fmri_valid_inputs:
print(">> Process fmri pipeline")
fmri_pipeline.process()
else:
print(" ... ERROR : Invalid inputs")
sys.exit(1)
fmri_pipeline.check_stages_execution()
fmri_pipeline.fill_stages_outputs()
else:
print(msg)
sys.exit(1)