def test_bids_naming():
from samri.pipelines.extra_functions import get_data_selection
from samri.pipelines.utils import bids_naming
import pandas as pd
import os
bruker_data_dir = path.join(DATA_DIR, 'bruker')
f_data_selection = get_data_selection(
bruker_data_dir,
match={
'task': ['JogB', 'CogB', 'CogB2m'],
},
)
s_data_selection = get_data_selection(
bruker_data_dir,
match={
'acquisition': ['TurboRARE', 'TurboRARElowcov'],
},
)
name = bids_naming(
subject_session=('5706', 'ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,
'sub-5706_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz',
debug=f_data_selection)
name = bids_naming(
subject_session=('4011', 'ofMaF'),
metadata=s_data_selection,
)
assert_and_feedback(name,
'sub-4011_ses-ofMaF_acq-TurboRARElowcov_T2w.nii.gz',
debug=s_data_selection)
name = bids_naming(
subject_session=('5704', 'ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,
'sub-5704_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz',
debug=f_data_selection)
name = bids_naming(
subject_session=('5704', 'ofMpF'),
metadata=s_data_selection,
)
assert_and_feedback(name,
'sub-5704_ses-ofMpF_acq-TurboRARE_T2w.nii.gz',
debug=s_data_selection)
def test_bids_naming():
from samri.pipelines.extra_functions import get_data_selection
from samri.pipelines.utils import bids_naming
import pandas as pd
import os
bruker_data_dir = path.join(DATA_DIR,'bruker')
f_data_selection = get_data_selection(bruker_data_dir,
match={
'task':['JogB','CogB','CogB2m'],
},
)
s_data_selection = get_data_selection(bruker_data_dir,
match={
'acquisition':['TurboRARE', 'TurboRARElowcov'],
},
)
name = bids_naming(
subject_session=('5706','ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,'sub-5706_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz', debug=f_data_selection)
name = bids_naming(
subject_session=('4011','ofMaF'),
metadata=s_data_selection,
)
assert_and_feedback(name,'sub-4011_ses-ofMaF_acq-TurboRARElowcov_T2w.nii.gz', debug=s_data_selection)
name = bids_naming(
subject_session=('5704','ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,'sub-5704_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz', debug=f_data_selection)
name = bids_naming(
subject_session=('5704','ofMpF'),
metadata=s_data_selection,
)
assert_and_feedback(name,'sub-5704_ses-ofMpF_acq-TurboRARE_T2w.nii.gz', debug=s_data_selection)
def bruker(
measurements_base,
template,
DEBUG=False,
exclude={},
functional_match={},
structural_match={},
sessions=[],
subjects=[],
actual_size=True,
functional_blur_xy=False,
functional_registration_method="structural",
highpass_sigma=225,
lowpass_sigma=None,
negative_contrast_agent=False,
n_procs=N_PROCS,
realign="time",
registration_mask=False,
tr=1,
very_nasty_bruker_delay_hack=False,
workflow_name="generic",
keep_work=False,
autorotate=False,
strict=False,
verbose=False,
):
'''
realign: {"space","time","spacetime",""}
Parameter that dictates slictiming correction and realignment of slices. "time" (FSL.SliceTimer) is default, since it works safely. Use others only with caution!
'''
if template:
if template == "mouse":
template = fetch_mouse_DSURQE()['template']
registration_mask = fetch_mouse_DSURQE()['mask']
elif template == "rat":
template = fetch_rat_waxholm()['template']
registration_mask = fetch_rat_waxholm()['mask']
else:
pass
else:
raise ValueError("No species or template specified")
return -1
measurements_base = path.abspath(path.expanduser(measurements_base))
# add subject and session filters if present
if subjects:
structural_scan_types['subject'] = subjects
if sessions:
structural_scan_types['session'] = sessions
# define measurement directories to be processed, and populate the list either with the given include_measurements, or with an intelligent selection
data_selection = pd.DataFrame([])
if structural_match:
s_data_selection = get_data_selection(
measurements_base,
match=structural_match,
exclude=exclude,
)
structural_scan_types = s_data_selection['scan_type'].unique()
data_selection = pd.concat([data_selection, s_data_selection])
if functional_match:
f_data_selection = get_data_selection(
measurements_base,
match=functional_match,
exclude=exclude,
)
functional_scan_types = f_data_selection['scan_type'].unique()
data_selection = pd.concat([data_selection, f_data_selection])
# we currently only support one structural scan type per session
#if functional_registration_method in ("structural", "composite") and structural_scan_types:
# structural_scan_types = [structural_scan_types[0]]
# we start to define nipype workflow elements (nodes, connections, meta)
subjects_sessions = data_selection[["subject", "session"
]].drop_duplicates().values.tolist()
if debug:
print('Data selection:')
print(data_selection)
print('Iterating over:')
print(subjects_sessions)
infosource = pe.Node(interface=util.IdentityInterface(
fields=['subject_session'], mandatory_inputs=False),
name="infosource")
infosource.iterables = [('subject_session', subjects_sessions)]
get_f_scan = pe.Node(name='get_f_scan',
interface=util.Function(
function=get_scan,
input_names=inspect.getargspec(get_scan)[0],
output_names=['scan_path', 'scan_type', 'trial']))
if not strict:
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = data_selection
get_f_scan.inputs.measurements_base = measurements_base
get_f_scan.iterables = ("scan_type", functional_scan_types)
f_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="f_bru2nii")
f_bru2nii.inputs.actual_size = actual_size
dummy_scans = pe.Node(
name='dummy_scans',
interface=util.Function(
function=force_dummy_scans,
input_names=inspect.getargspec(force_dummy_scans)[0],
output_names=['out_file']))
dummy_scans.inputs.desired_dummy_scans = DUMMY_SCANS
bandpass = pe.Node(interface=fsl.maths.TemporalFilter(), name="bandpass")
bandpass.inputs.highpass_sigma = highpass_sigma
if lowpass_sigma:
bandpass.inputs.lowpass_sigma = lowpass_sigma
else:
bandpass.inputs.lowpass_sigma = tr
#bids_filename = pe.Node(name='bids_filename', interface=util.Function(function=sss_filename,input_names=inspect.getargspec(sss_filename)[0], output_names=['filename']))
bids_filename = pe.Node(name='bids_filename',
interface=util.Function(
function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
bids_filename.inputs.metadata = data_selection
#bids_stim_filename = pe.Node(name='bids_stim_filename', interface=util.Function(function=sss_filename,input_names=inspect.getargspec(sss_filename)[0], output_names=['filename']))
bids_stim_filename = pe.Node(
name='bids_stim_filename',
interface=util.Function(function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
bids_stim_filename.inputs.suffix = "events"
bids_stim_filename.inputs.extension = ".tsv"
bids_stim_filename.inputs.metadata = data_selection
events_file = pe.Node(
name='events_file',
interface=util.Function(
function=write_events_file,
input_names=inspect.getargspec(write_events_file)[0],
output_names=['out_file']))
events_file.inputs.dummy_scans_ms = DUMMY_SCANS * tr * 1000
events_file.inputs.stim_protocol_dictionary = STIM_PROTOCOL_DICTIONARY
events_file.inputs.very_nasty_bruker_delay_hack = very_nasty_bruker_delay_hack
if not (strict or verbose):
events_file.inputs.ignore_exception = True
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = path.join(measurements_base,
"preprocessing", workflow_name)
datasink.inputs.parameterization = False
if not (strict or verbose):
datasink.inputs.ignore_exception = True
workflow_connections = [
(infosource, get_f_scan, [('subject_session', 'selector')]),
(infosource, bids_stim_filename, [('subject_session',
'subject_session')]),
(get_f_scan, bids_stim_filename, [('scan_type', 'scan_type')]),
(get_f_scan, f_bru2nii, [('scan_path', 'input_dir')]),
(f_bru2nii, dummy_scans, [('nii_file', 'in_file')]),
(get_f_scan, dummy_scans, [('scan_path', 'scan_dir')]),
(get_f_scan, events_file, [('trial', 'trial'),
('scan_path', 'scan_dir')]),
(events_file, datasink, [('out_file', 'func.@events')]),
(bids_stim_filename, events_file, [('filename', 'out_file')]),
(infosource, datasink, [(('subject_session', ss_to_path), 'container')
]),
(infosource, bids_filename, [('subject_session', 'subject_session')]),
(get_f_scan, bids_filename, [('scan_type', 'scan_type')]),
(bids_filename, bandpass, [('filename', 'out_file')]),
(bandpass, datasink, [('out_file', 'func')]),
]
if realign == "space":
realigner = pe.Node(interface=spm.Realign(), name="realigner")
realigner.inputs.register_to_mean = True
workflow_connections.extend([
(dummy_scans, realigner, [('out_file', 'in_file')]),
])
elif realign == "spacetime":
realigner = pe.Node(interface=nipy.SpaceTimeRealigner(),
name="realigner")
realigner.inputs.slice_times = "asc_alt_2"
realigner.inputs.tr = tr
realigner.inputs.slice_info = 3 #3 for coronal slices (2 for horizontal, 1 for sagittal)
workflow_connections.extend([
(dummy_scans, realigner, [('out_file', 'in_file')]),
])
elif realign == "time":
realigner = pe.Node(interface=fsl.SliceTimer(), name="slicetimer")
realigner.inputs.time_repetition = tr
workflow_connections.extend([
(dummy_scans, realigner, [('out_file', 'in_file')]),
])
#ADDING SELECTABLE NODES AND EXTENDING WORKFLOW AS APPROPRIATE:
if actual_size:
s_biascorrect, f_biascorrect = real_size_nodes()
else:
s_biascorrect, f_biascorrect = inflated_size_nodes()
if structural_scan_types.any():
get_s_scan = pe.Node(
name='get_s_scan',
interface=util.Function(
function=get_scan,
input_names=inspect.getargspec(get_scan)[0],
output_names=['scan_path', 'scan_type', 'trial']))
if not strict:
get_s_scan.inputs.ignore_exception = True
get_s_scan.inputs.data_selection = data_selection
get_s_scan.inputs.measurements_base = measurements_base
get_s_scan.iterables = ("scan_type", structural_scan_types)
s_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="s_bru2nii")
s_bru2nii.inputs.force_conversion = True
s_bru2nii.inputs.actual_size = actual_size
#s_bids_filename = pe.Node(name='s_bids_filename', interface=util.Function(function=sss_filename,input_names=inspect.getargspec(sss_filename)[0], output_names=['filename']))
s_bids_filename = pe.Node(
name='s_bids_filename',
interface=util.Function(
function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
s_bids_filename.inputs.metadata = data_selection
if actual_size:
s_register, s_warp, _, _ = DSURQEc_structural_registration(
template, registration_mask)
#TODO: incl. in func registration
if autorotate:
workflow_connections.extend([
(s_biascorrect, s_rotated, [('output_image', 'out_file')]),
(s_rotated, s_register, [('out_file', 'moving_image')]),
])
else:
workflow_connections.extend([
(s_biascorrect, s_register, [('output_image',
'moving_image')]),
(s_register, s_warp, [('composite_transform', 'transforms')
]),
(s_bru2nii, s_warp, [('nii_file', 'input_image')]),
(s_warp, datasink, [('output_image', 'anat')]),
])
else:
s_reg_biascorrect = pe.Node(interface=ants.N4BiasFieldCorrection(),
name="s_reg_biascorrect")
s_reg_biascorrect.inputs.dimension = 3
s_reg_biascorrect.inputs.bspline_fitting_distance = 95
s_reg_biascorrect.inputs.shrink_factor = 2
s_reg_biascorrect.inputs.n_iterations = [500, 500, 500, 500]
s_reg_biascorrect.inputs.convergence_threshold = 1e-14
s_cutoff = pe.Node(interface=fsl.ImageMaths(), name="s_cutoff")
s_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
s_BET = pe.Node(interface=fsl.BET(), name="s_BET")
s_BET.inputs.mask = True
s_BET.inputs.frac = 0.3
s_BET.inputs.robust = True
s_mask = pe.Node(interface=fsl.ApplyMask(), name="s_mask")
s_register, s_warp, f_warp = structural_registration(template)
workflow_connections.extend([
(s_bru2nii, s_reg_biascorrect, [('nii_file', 'input_image')]),
(s_reg_biascorrect, s_cutoff, [('output_image', 'in_file')]),
(s_cutoff, s_BET, [('out_file', 'in_file')]),
(s_biascorrect, s_mask, [('output_image', 'in_file')]),
(s_BET, s_mask, [('mask_file', 'mask_file')]),
])
#TODO: incl. in func registration
if autorotate:
workflow_connections.extend([
(s_mask, s_rotated, [('out_file', 'out_file')]),
(s_rotated, s_register, [('out_file', 'moving_image')]),
])
else:
workflow_connections.extend([
(s_mask, s_register, [('out_file', 'moving_image')]),
(s_register, s_warp, [('composite_transform', 'transforms')
]),
(s_bru2nii, s_warp, [('nii_file', 'input_image')]),
(s_warp, datasink, [('output_image', 'anat')]),
])
if autorotate:
s_rotated = autorotate(template)
workflow_connections.extend([
(infosource, get_s_scan, [('subject_session', 'selector')]),
(infosource, s_bids_filename, [('subject_session',
'subject_session')]),
(get_s_scan, s_bru2nii, [('scan_path', 'input_dir')]),
(get_s_scan, s_bids_filename, [('scan_type', 'scan_type')]),
(s_bids_filename, s_warp, [('filename', 'output_image')]),
(s_bru2nii, s_biascorrect, [('nii_file', 'input_image')]),
])
if functional_registration_method == "structural":
if not structural_scan_types:
raise ValueError(
'The option `registration="structural"` requires there to be a structural scan type.'
)
workflow_connections.extend([
(s_register, f_warp, [('composite_transform', 'transforms')]),
])
if realign == "space":
workflow_connections.extend([
(realigner, f_warp, [('realigned_files', 'input_image')]),
])
elif realign == "spacetime":
workflow_connections.extend([
(realigner, f_warp, [('out_file', 'input_image')]),
])
elif realign == "time":
workflow_connections.extend([
(realigner, f_warp, [('slice_time_corrected_file',
'input_image')]),
])
else:
workflow_connections.extend([
(dummy_scans, f_warp, [('out_file', 'input_image')]),
])
if functional_registration_method == "composite":
if not structural_scan_types.any():
raise ValueError(
'The option `registration="composite"` requires there to be a structural scan type.'
)
_, _, f_register, f_warp = DSURQEc_structural_registration(
template, registration_mask)
temporal_mean = pe.Node(interface=fsl.MeanImage(),
name="temporal_mean")
merge = pe.Node(util.Merge(2), name='merge')
workflow_connections.extend([
(temporal_mean, f_biascorrect, [('out_file', 'input_image')]),
(f_biascorrect, f_register, [('output_image', 'moving_image')]),
(s_biascorrect, f_register, [('output_image', 'fixed_image')]),
(f_register, merge, [('composite_transform', 'in1')]),
(s_register, merge, [('composite_transform', 'in2')]),
(merge, f_warp, [('out', 'transforms')]),
])
if realign == "space":
workflow_connections.extend([
(realigner, temporal_mean, [('realigned_files', 'in_file')]),
(realigner, f_warp, [('realigned_files', 'input_image')]),
])
elif realign == "spacetime":
workflow_connections.extend([
(realigner, temporal_mean, [('out_file', 'in_file')]),
(realigner, f_warp, [('out_file', 'input_image')]),
])
elif realign == "time":
workflow_connections.extend([
(realigner, temporal_mean, [('slice_time_corrected_file',
'in_file')]),
(realigner, f_warp, [('slice_time_corrected_file',
'input_image')]),
])
else:
workflow_connections.extend([
(dummy_scans, temporal_mean, [('out_file', 'in_file')]),
(dummy_scans, f_warp, [('out_file', 'input_image')]),
])
elif functional_registration_method == "functional":
f_register, f_warp = functional_registration(template)
temporal_mean = pe.Node(interface=fsl.MeanImage(),
name="temporal_mean")
#f_cutoff = pe.Node(interface=fsl.ImageMaths(), name="f_cutoff")
#f_cutoff.inputs.op_string = "-thrP 30"
#f_BET = pe.Node(interface=fsl.BET(), name="f_BET")
#f_BET.inputs.mask = True
#f_BET.inputs.frac = 0.5
workflow_connections.extend([
(temporal_mean, f_biascorrect, [('out_file', 'input_image')]),
#(f_biascorrect, f_cutoff, [('output_image', 'in_file')]),
#(f_cutoff, f_BET, [('out_file', 'in_file')]),
#(f_BET, f_register, [('out_file', 'moving_image')]),
(f_biascorrect, f_register, [('output_image', 'moving_image')]),
(f_register, f_warp, [('composite_transform', 'transforms')]),
])
if realign == "space":
workflow_connections.extend([
(realigner, temporal_mean, [('realigned_files', 'in_file')]),
(realigner, f_warp, [('realigned_files', 'input_image')]),
])
elif realign == "spacetime":
workflow_connections.extend([
(realigner, temporal_mean, [('out_file', 'in_file')]),
(realigner, f_warp, [('out_file', 'input_image')]),
])
elif realign == "time":
workflow_connections.extend([
(realigner, temporal_mean, [('slice_time_corrected_file',
'in_file')]),
(realigner, f_warp, [('slice_time_corrected_file',
'input_image')]),
])
else:
workflow_connections.extend([
(dummy_scans, temporal_mean, [('out_file', 'in_file')]),
(dummy_scans, f_warp, [('out_file', 'input_image')]),
])
invert = pe.Node(interface=fsl.ImageMaths(), name="invert")
if functional_blur_xy and negative_contrast_agent:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(f_warp, blur, [('output_image', 'in_file')]),
(blur, invert, [(('out_file', fslmaths_invert_values), 'op_string')
]),
(blur, invert, [('out_file', 'in_file')]),
(invert, bandpass, [('out_file', 'in_file')]),
])
elif functional_blur_xy:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(f_warp, blur, [('output_image', 'in_file')]),
(blur, bandpass, [('out_file', 'in_file')]),
])
elif negative_contrast_agent:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(f_warp, invert, [(('output_image', fslmaths_invert_values),
'op_string')]),
(f_warp, invert, [('output_image', 'in_file')]),
(invert, bandpass, [('out_file', 'in_file')]),
])
else:
workflow_connections.extend([
(f_warp, bandpass, [('output_image', 'in_file')]),
])
workflow_config = {
'execution': {
'crashdump_dir':
path.join(measurements_base, 'preprocessing/crashdump'),
}
}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workdir_name = workflow_name + "_work"
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(measurements_base, "preprocessing")
workflow.config = workflow_config
workflow.write_graph(dotfilename=path.join(workflow.base_dir, workdir_name,
"graph.dot"),
graph2use="hierarchical",
format="png")
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir, workdir_name))
def bru2bids(
measurements_base,
bids_extra=['acq', 'run'],
dataset_authors=[],
dataset_license='',
dataset_name=False,
debug=False,
diffusion_match={},
exclude={},
functional_match={},
inflated_size=False,
keep_crashdump=False,
keep_work=False,
measurements=[],
n_procs=N_PROCS,
out_base=None,
structural_match={},
workflow_name='bids',
):
"""
Convert and reorganize Bruker "raw" directories (2dseq and ParaVision-formatted metadata files) into a BIDS-organized file hierarchy containing NIfTI files and associated metadata.
If any exist, this workflow also reposits COSplay event files (already written according to BIDS) in the correct place in the output hierarchy.
Parameters
----------
measurements_base : str
Path of the top level directory containing all the Bruker ParaVision scan directories to be converted and reformatted.
bids_extra : list, optional
List of strings denoting optional BIDS fields to include in the resulting file names.
Accepted items are 'acq' and 'run'.
dataset_authors : list of string, optional
A list of dataset author names, which will be written into the BIDS metadata file.
Generally not needed, unless this is important for you.
dataset_license : string, optional
A dataset license name that will be written into the BIDS metadata file.
Generally not needed, unless this is important for you.
dataset_name : string, optional
A dataset name that will be written into the BIDS metadata file.
Generally not needed, as by default we use the dataset path to satisfy this BIDS requirement.
debug : bool, optional
Whether to enable debug support.
This prints the data selection before passing it to the nipype workflow management system, and turns on debug support in nipype (leading to more verbose logging).
diffusion_match : dict, optional
A dictionary with any combination of "session", "subject", "task", and "acquisition" as keys and corresponding lists of identifiers as values.
Only diffusion scans matching all identifiers will be included - i.e. this is a whitelist.
exclude : dict, optional
A dictionary with any combination of "session", "subject", "task" , and "acquisition" as keys and corresponding identifiers as values.
Only scans not matching any of the listed criteria will be included in the workfolow - i.e. this is a blacklist (for functional and structural scans).
functional_match : dict, optional
A dictionary with any combination of "session", "subject", "task", and "acquisition" as keys and corresponding lists of identifiers as values.
Only Functional scans matching all identifiers will be included - i.e. this is a whitelist.
inflated_size : bool, optional
Whether to inflate the voxel size reported by the scanner when converting the data to NIfTI.
Setting this to `True` multiplies the voxel edge lengths by 10 (i.e. the volume by 1000); this is occasionally done in some small animal pipelines, which use routines designed exclusively for human data.
Unless you are looking to reproduce such a workflow, this should be set to `True`.
keep_crashdump : bool, optional
Whether to keep the crashdump directory (containing all the crash reports for intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
keep_work : bool, optional
Whether to keep the work directory (containing all the intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
measurements : list, optional
Whitelist of Bruker ParaVision scan directories to consider.
n_procs : int, optional
Maximum number of processes which to simultaneously spawn for the workflow.
If not explicitly defined, this is automatically calculated from the number of available cores and under the assumption that the workflow will be the main process running for the duration that it is running.
out_base : str, optional
Base directory in which to place the BIDS reposited data.
If not present the BIDS records will be created in the `measurements_base` directory.
structural_match : dict, optional
A dictionary with any combination of "session", "subject", "task", and "acquisition" as keys and corresponding lists of identifiers as values.
Only structural scans matching all identifiers will be included - i.e. this is a whitelist.
workflow_name : str, optional
Top level name for the output directory.
"""
measurements_base = path.abspath(path.expanduser(measurements_base))
if out_base:
out_base = path.abspath(path.expanduser(out_base))
else:
out_base = measurements_base
out_dir = path.join(out_base, workflow_name)
workdir_name = workflow_name + '_work'
workdir = path.join(out_base, workdir_name)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
# This is needed because BIDS does not yet support CBV
with open(path.join(out_dir, ".bidsignore"), "w+") as f:
f.write('*_cbv.*')
# BIDS needs a descriptor file
if not dataset_name:
dataset_name = measurements_base
description = {
'Name': dataset_name,
'BIDSVersion': '1.2.0',
}
if dataset_authors:
description['Authors'] = dataset_authors
if dataset_license:
description['License'] = dataset_license
with open(path.join(out_dir, 'dataset_description.json'), 'w') as f:
json.dump(description, f, indent=1)
f.write("\n")
# define measurement directories to be processed, and populate the list either with the given include_measurements, or with an intelligent selection
functional_scan_types = diffusion_scan_types = structural_scan_types = []
data_selection = pd.DataFrame([])
if structural_match:
s_data_selection = get_data_selection(
measurements_base,
match=structural_match,
exclude=exclude,
measurements=measurements,
)
print(s_data_selection.columns)
structural_scan_types = list(s_data_selection['scan_type'].unique())
struct_ind = s_data_selection.index.tolist()
data_selection = pd.concat([data_selection, s_data_selection],
sort=True)
if functional_match:
f_data_selection = get_data_selection(
measurements_base,
match=functional_match,
exclude=exclude,
measurements=measurements,
)
print(f_data_selection)
functional_scan_types = list(f_data_selection['scan_type'].unique())
func_ind = f_data_selection.index.tolist()
data_selection = pd.concat([data_selection, f_data_selection],
sort=True)
if diffusion_match:
d_data_selection = get_data_selection(
measurements_base,
match=diffusion_match,
exclude=exclude,
measurements=measurements,
)
diffusion_scan_types = list(d_data_selection['scan_type'].unique())
dwi_ind = d_data_selection.index.tolist()
data_selection = pd.concat([data_selection, d_data_selection],
sort=True)
# we start to define nipype workflow elements (nodes, connections, meta)
subjects_sessions = data_selection[["subject", "session"
]].drop_duplicates().values.tolist()
if debug:
print('Data selection:')
print(data_selection)
print('Iterating over:')
print(subjects_sessions)
infosource = pe.Node(interface=util.IdentityInterface(
fields=['subject_session'], mandatory_inputs=False),
name="infosource")
infosource.iterables = [('subject_session', subjects_sessions)]
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = out_dir
datasink.inputs.parameterization = False
workflow_connections = [
(infosource, datasink, [(('subject_session', ss_to_path), 'container')
]),
]
if functional_scan_types:
if not os.path.exists(workdir):
os.makedirs(workdir)
f_data_selection.to_csv(path.join(workdir, 'f_data_selection.csv'))
get_f_scan = pe.Node(
name='get_f_scan',
interface=util.Function(
function=get_bids_scan,
input_names=inspect.getargspec(get_bids_scan)[0],
output_names=[
'scan_path',
'typ',
'task',
'nii_path',
'nii_name',
'eventfile_name',
'subject_session',
'metadata_filename',
'dict_slice',
'ind_type',
]))
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = f_data_selection
get_f_scan.inputs.bids_base = measurements_base
get_f_scan.iterables = ("ind_type", func_ind)
f_bru2nii = pe.Node(interface=Bru2(), name="f_bru2nii")
f_bru2nii.inputs.actual_size = not inflated_size
f_bru2nii.inputs.compress = True
f_metadata_file = pe.Node(
name='metadata_file',
interface=util.Function(
function=write_bids_metadata_file,
input_names=inspect.getargspec(write_bids_metadata_file)[0],
output_names=['out_file']))
f_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
f_flip = pe.Node(name='f_flip',
interface=util.Function(
function=flip_if_needed,
input_names=inspect.getargspec(flip_if_needed)[0],
output_names=['out_file']))
f_flip.inputs.data_selection = f_data_selection
events_file = pe.Node(
name='events_file',
interface=util.Function(
function=write_bids_events_file,
input_names=inspect.getargspec(write_bids_events_file)[0],
output_names=['out_file']))
events_file.ignore_exception = True
physio_file = pe.Node(
name='physio_file',
interface=util.Function(
function=write_bids_physio_file,
input_names=inspect.getargspec(write_bids_physio_file)[0],
output_names=['out_file', 'out_metadata_file']))
workflow_connections = [
(get_f_scan, datasink, [(('subject_session', ss_to_path),
'container')]),
(get_f_scan, f_bru2nii, [('scan_path', 'input_dir')]),
(get_f_scan, f_bru2nii, [('nii_name', 'output_filename')]),
(get_f_scan, f_flip, [('ind_type', 'ind')]),
(get_f_scan, f_flip, [('nii_name', 'output_filename')]),
(f_bru2nii, f_flip, [('nii_file', 'nii_path')]),
(f_flip, datasink, [('out_file', 'func')]),
(f_metadata_file, events_file, [('out_file', 'metadata_file')]),
(f_bru2nii, events_file, [('nii_file', 'timecourse_file')]),
(get_f_scan, f_metadata_file, [('metadata_filename', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')]),
(get_f_scan, events_file, [('eventfile_name', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')]),
(get_f_scan, physio_file, [('nii_name', 'nii_name'),
('scan_path', 'scan_dir')]),
(events_file, datasink, [('out_file', 'func.@events')]),
(physio_file, datasink, [('out_file', 'func.@physio')]),
(physio_file, datasink, [('out_metadata_file', 'func.@meta_physio')
]),
(f_metadata_file, datasink, [('out_file', 'func.@metadata')]),
]
crashdump_dir = path.join(out_base, workflow_name + '_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(out_base)
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,
workdir_name,
"graph_functional.dot"),
graph2use="hierarchical",
format="png")
except OSError:
print(
'We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.'
)
#Execute the workflow
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc",
plugin_args={'n_procs': n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir, workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except (FileNotFoundError, OSError):
pass
if diffusion_scan_types:
# We check for the directory, since it gets deleted after a successful execution.
if not os.path.exists(workdir):
os.makedirs(workdir)
d_data_selection.to_csv(path.join(workdir, 'd_data_selection.csv'))
get_d_scan = pe.Node(
name='get_d_scan',
interface=util.Function(
function=get_bids_scan,
input_names=inspect.getargspec(get_bids_scan)[0],
output_names=[
'scan_path',
'typ',
'task',
'nii_path',
'nii_name',
'eventfile_name',
'subject_session',
'metadata_filename',
'dict_slice',
'ind_type',
]))
get_d_scan.inputs.ignore_exception = True
get_d_scan.inputs.data_selection = d_data_selection
get_d_scan.inputs.extra = ['acq']
get_d_scan.inputs.bids_base = measurements_base
get_d_scan.iterables = ("ind_type", dwi_ind)
d_bru2nii = pe.Node(interface=Bru2(), name="d_bru2nii")
d_bru2nii.inputs.force_conversion = True
d_bru2nii.inputs.actual_size = not inflated_size
d_bru2nii.inputs.compress = True
d_metadata_file = pe.Node(
name='metadata_file',
interface=util.Function(
function=write_bids_metadata_file,
input_names=inspect.getargspec(write_bids_metadata_file)[0],
output_names=['out_file']))
d_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
workflow_connections = [
(get_d_scan, datasink, [(('subject_session', ss_to_path),
'container')]),
(get_d_scan, d_bru2nii, [('scan_path', 'input_dir')]),
(get_d_scan, d_bru2nii, [('nii_name', 'output_filename')]),
(d_bru2nii, datasink, [('nii_file', 'dwi')]),
(get_d_scan, d_metadata_file, [('metadata_filename', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')]),
(d_metadata_file, datasink, [('out_file', 'dwi.@metadata')]),
]
crashdump_dir = path.join(out_base, workflow_name + '_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(out_base)
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,
workdir_name,
"graph_diffusion.dot"),
graph2use="hierarchical",
format="png")
except OSError:
print(
'We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.'
)
#Execute the workflow
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc",
plugin_args={'n_procs': n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir, workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except (FileNotFoundError, OSError):
pass
if structural_scan_types:
# We check for the directory, since it gets deleted after a successful execution.
if not os.path.exists(workdir):
os.makedirs(workdir)
s_data_selection.to_csv(path.join(workdir, 's_data_selection.csv'))
get_s_scan = pe.Node(
name='get_s_scan',
interface=util.Function(
function=get_bids_scan,
input_names=inspect.getargspec(get_bids_scan)[0],
output_names=[
'scan_path',
'typ',
'task',
'nii_path',
'nii_name',
'eventfile_name',
'subject_session',
'metadata_filename',
'dict_slice',
'ind_type',
]))
get_s_scan.inputs.ignore_exception = True
get_s_scan.inputs.data_selection = s_data_selection
get_s_scan.inputs.extra = ['acq']
get_s_scan.inputs.bids_base = measurements_base
get_s_scan.iterables = ("ind_type", struct_ind)
s_bru2nii = pe.Node(interface=Bru2(), name="s_bru2nii")
s_bru2nii.inputs.force_conversion = True
s_bru2nii.inputs.actual_size = not inflated_size
s_bru2nii.inputs.compress = True
s_metadata_file = pe.Node(
name='metadata_file',
interface=util.Function(
function=write_bids_metadata_file,
input_names=inspect.getargspec(write_bids_metadata_file)[0],
output_names=['out_file']))
s_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
s_flip = pe.Node(name='s_flip',
interface=util.Function(
function=flip_if_needed,
input_names=inspect.getargspec(flip_if_needed)[0],
output_names=['out_file']))
s_flip.inputs.data_selection = s_data_selection
workflow_connections = [
(get_s_scan, datasink, [(('subject_session', ss_to_path),
'container')]),
(get_s_scan, s_bru2nii, [('scan_path', 'input_dir')]),
(get_s_scan, s_bru2nii, [('nii_name', 'output_filename')]),
(get_s_scan, s_flip, [('ind_type', 'ind')]),
(get_s_scan, s_flip, [('nii_name', 'output_filename')]),
(s_bru2nii, s_flip, [('nii_file', 'nii_path')]),
(s_flip, datasink, [('out_file', 'anat')]),
(get_s_scan, s_metadata_file, [('metadata_filename', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')]),
(s_metadata_file, datasink, [('out_file', 'anat.@metadata')]),
]
crashdump_dir = path.join(out_base, workflow_name + '_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(out_base)
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,
workdir_name,
"graph_structural.dot"),
graph2use="hierarchical",
format="png")
except OSError:
print(
'We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.'
)
#Execute the workflow
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc",
plugin_args={'n_procs': n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir, workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except (FileNotFoundError, OSError):
pass
# Create essions files
sessions_file(out_dir, data_selection)
# Introduce the notion of validation:
print(
'\n'
'USER NOTICE:\n'
'To ensure conformity with the most recent release of the BIDS standard, you may want to submit the dataset to the online\n'
'validator (this will *not* require you to actually upload any of the data):\n'
'https://bids-standard.github.io/bids-validator/')
def bru2bids(
measurements_base,
measurements=[],
actual_size=True,
debug=False,
exclude={},
functional_match={},
keep_crashdump=False,
keep_work=False,
n_procs=N_PROCS,
structural_match={},
):
"""
Convert and reorganize Bruker "raw" directories (2dseq and ParaVision-formatted metadata files) into a BIDS-organized file hierarchy containing NIfTI files and associated metadata.
If any exist, this workflow also reposits COSplay event files (already written according to BIDS) in the correct place in the output hierarchy.
Parameters
----------
measurements_base : str
Path of the top level directory containing all the Bruker scan directories to be converted and reformatted.
actual_size : bool, optional
Whether to conserve the voxel size reported by the scanner when converting the data to NIfTI.
Setting this to `False` multiplies the voxel edge lengths by 10 (i.e. the volume by 1000); this is occasionally done in hackish small animal pipelines, which use routines designed exclusively for human data.
Unless you are looking to reproduce such a workflow, this should be set to `True`.
debug : bool, optional
Whether to enable debug support.
This prints the data selection before passing it to the nipype workflow management system, and turns on debug support in nipype (leading to more verbose logging).
exclude : dict, optional
A dictionary with any combination of "session", "subject", "trial" , and "acquisition" as keys and corresponding identifiers as values.
Only scans not matching any of the listed criteria will be included in the workfolow - i.e. this is a blacklist (for functional and structural scans).
functional_match : dict, optional
A dictionary with any combination of "session", "subject", "trial", and "acquisition" as keys and corresponding lists of identifiers as values.
Functional scans matching all identifiers will be included - i.e. this is a whitelist.
keep_work : bool, optional
Whether to keep the work directory (containing all the intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
keep_crashdump : bool, optional
Whether to keep the crashdump directory (containing all the crash reports for intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
n_procs : int, optional
Maximum number of processes which to simultaneously spawn for the workflow.
If not explicitly defined, this is automatically calculated from the number of available cores and under the assumption that the workflow will be the main process running for the duration that it is running.
structural_match : dict, optional
A dictionary with any combination of "session", "subject", "trial", and "acquisition" as keys and corresponding lists of identifiers as values.
Functional scans matching all identifiers will be included - i.e. this is a whitelist.
"""
measurements_base = path.abspath(path.expanduser(measurements_base))
# define measurement directories to be processed, and populate the list either with the given include_measurements, or with an intelligent selection
data_selection = pd.DataFrame([])
if structural_match:
s_data_selection = get_data_selection(
measurements_base,
match=structural_match,
exclude=exclude,
measurements=measurements,
)
structural_scan_types = s_data_selection['scan_type'].unique()
data_selection = pd.concat([data_selection, s_data_selection])
if functional_match:
f_data_selection = get_data_selection(
measurements_base,
match=functional_match,
exclude=exclude,
measurements=measurements,
)
functional_scan_types = f_data_selection['scan_type'].unique()
data_selection = pd.concat([data_selection, f_data_selection])
# we start to define nipype workflow elements (nodes, connections, meta)
subjects_sessions = data_selection[["subject", "session"
]].drop_duplicates().values.tolist()
if debug:
print('Data selection:')
print(data_selection)
print('Iterating over:')
print(subjects_sessions)
infosource = pe.Node(interface=util.IdentityInterface(
fields=['subject_session'], mandatory_inputs=False),
name="infosource")
infosource.iterables = [('subject_session', subjects_sessions)]
get_f_scan = pe.Node(name='get_f_scan',
interface=util.Function(
function=get_scan,
input_names=inspect.getargspec(get_scan)[0],
output_names=['scan_path', 'scan_type', 'trial']))
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = data_selection
get_f_scan.inputs.measurements_base = measurements_base
get_f_scan.iterables = ("scan_type", functional_scan_types)
f_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="f_bru2nii")
f_bru2nii.inputs.actual_size = actual_size
f_filename = pe.Node(name='f_filename',
interface=util.Function(
function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
f_filename.inputs.metadata = data_selection
f_filename.inputs.extension = ''
f_metadata_filename = pe.Node(
name='f_metadata_filename',
interface=util.Function(function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
f_metadata_filename.inputs.extension = ".json"
f_metadata_filename.inputs.metadata = data_selection
events_filename = pe.Node(
name='bids_stim_filename',
interface=util.Function(function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
events_filename.inputs.suffix = "events"
events_filename.inputs.extension = ".tsv"
events_filename.inputs.metadata = data_selection
events_filename.ignore_exception = True
f_metadata_file = pe.Node(
name='metadata_file',
interface=util.Function(
function=write_bids_metadata_file,
input_names=inspect.getargspec(write_bids_metadata_file)[0],
output_names=['out_file']))
f_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
events_file = pe.Node(
name='events_file',
interface=util.Function(
function=write_events_file,
input_names=inspect.getargspec(write_events_file)[0],
output_names=['out_file']))
events_file.ignore_exception = True
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = path.join(measurements_base, "bids")
datasink.inputs.parameterization = False
workflow_connections = [
(infosource, datasink, [(('subject_session', ss_to_path), 'container')
]),
(infosource, get_f_scan, [('subject_session', 'selector')]),
(infosource, f_metadata_filename, [('subject_session',
'subject_session')]),
(infosource, f_filename, [('subject_session', 'subject_session')]),
(infosource, events_filename, [('subject_session', 'subject_session')
]),
(get_f_scan, f_metadata_filename, [('scan_type', 'scan_type')]),
(get_f_scan, f_filename, [('scan_type', 'scan_type')]),
(get_f_scan, f_bru2nii, [('scan_path', 'input_dir')]),
(get_f_scan, f_metadata_file, [('scan_path', 'scan_dir')]),
(f_metadata_filename, f_metadata_file, [('filename', 'out_file')]),
(f_filename, f_bru2nii, [('filename', 'output_filename')]),
(events_filename, events_file, [('filename', 'out_file')]),
(f_metadata_file, events_file, [('out_file', 'metadata_file')]),
(f_bru2nii, events_file, [('nii_file', 'timecourse_file')]),
(get_f_scan, events_filename, [('scan_type', 'scan_type')]),
(f_bru2nii, datasink, [('nii_file', 'func')]),
(get_f_scan, events_file, [('trial', 'trial'),
('scan_path', 'scan_dir')]),
(events_file, datasink, [('out_file', 'func.@events')]),
(f_metadata_file, datasink, [('out_file', 'func.@metadata')]),
]
crashdump_dir = path.join(measurements_base, 'bids_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workdir_name = 'bids_work'
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(measurements_base)
workflow.config = workflow_config
workflow.write_graph(dotfilename=path.join(workflow.base_dir, workdir_name,
"graph.dot"),
graph2use="hierarchical",
format="png")
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs': n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir, workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except FileNotFoundError:
pass
try:
if structural_scan_types.any():
get_s_scan = pe.Node(
name='get_s_scan',
interface=util.Function(
function=get_scan,
input_names=inspect.getargspec(get_scan)[0],
output_names=['scan_path', 'scan_type', 'trial']))
get_s_scan.inputs.ignore_exception = True
get_s_scan.inputs.data_selection = data_selection
get_s_scan.inputs.measurements_base = measurements_base
get_s_scan.iterables = ("scan_type", structural_scan_types)
s_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="s_bru2nii")
s_bru2nii.inputs.force_conversion = True
s_bru2nii.inputs.actual_size = actual_size
s_filename = pe.Node(
name='s_filename',
interface=util.Function(
function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
s_filename.inputs.metadata = data_selection
s_filename.inputs.extension = ''
s_metadata_filename = pe.Node(
name='s_metadata_filename',
interface=util.Function(
function=bids_naming,
input_names=inspect.getargspec(bids_naming)[0],
output_names=['filename']))
s_metadata_filename.inputs.extension = ".json"
s_metadata_filename.inputs.metadata = data_selection
s_metadata_file = pe.Node(name='s_metadata_file',
interface=util.Function(
function=write_bids_metadata_file,
input_names=inspect.getargspec(
write_bids_metadata_file)[0],
output_names=['out_file']))
s_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
workflow_connections = [
(infosource, datasink, [(('subject_session', ss_to_path),
'container')]),
(infosource, get_s_scan, [('subject_session', 'selector')]),
(infosource, s_filename, [('subject_session',
'subject_session')]),
(infosource, s_metadata_filename, [('subject_session',
'subject_session')]),
(get_s_scan, s_bru2nii, [('scan_path', 'input_dir')]),
(get_s_scan, s_filename, [('scan_type', 'scan_type')]),
(get_s_scan, s_metadata_filename, [('scan_type', 'scan_type')
]),
(get_s_scan, s_metadata_file, [('scan_path', 'scan_dir')]),
(s_filename, s_bru2nii, [('filename', 'output_filename')]),
(s_metadata_filename, s_metadata_file, [('filename',
'out_file')]),
(s_bru2nii, datasink, [('nii_file', 'anat')]),
(s_metadata_file, datasink, [('out_file', 'anat.@metadata')]),
]
crashdump_dir = path.join(measurements_base, 'bids_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level': 'DEBUG',
'utils_level': 'DEBUG',
'interface_level': 'DEBUG',
'filemanip_level': 'DEBUG',
'log_to_file': 'true',
}
workdir_name = 'bids_work'
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(measurements_base)
workflow.config = workflow_config
workflow.write_graph(dotfilename=path.join(workflow.base_dir,
workdir_name,
"graph.dot"),
graph2use="hierarchical",
format="png")
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc",
plugin_args={'n_procs': n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc",
plugin_args={'n_procs': n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir, workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except FileNotFoundError:
pass
except UnboundLocalError:
pass
def bruker(measurements_base,
functional_scan_types=[],
structural_scan_types=[],
sessions=[],
subjects=[],
measurements=[],
exclude_subjects=[],
exclude_measurements=[],
actual_size=False,
functional_blur_xy=False,
functional_registration_method="structural",
highpass_sigma=225,
lowpass_sigma=None,
negative_contrast_agent=False,
n_procs=N_PROCS,
realign=True,
registration_mask=False,
template="/home/chymera/ni_data/templates/ds_QBI_chr.nii.gz",
tr=1,
very_nasty_bruker_delay_hack=False,
workflow_name="generic",
keep_work=False,
autorotate=False,
strict=False,
):
measurements_base = os.path.abspath(os.path.expanduser(measurements_base))
#select all functional/sturctural scan types unless specified
if not functional_scan_types or not structural_scan_types:
scan_classification = pd.read_csv(scan_classification_file_path)
if not functional_scan_types:
functional_scan_types = list(scan_classification[(scan_classification["categories"] == "functional")]["scan_type"])
if not structural_scan_types:
structural_scan_types = list(scan_classification[(scan_classification["categories"] == "structural")]["scan_type"])
#hack to allow structural scan type disabling:
if structural_scan_types == -1:
structural_scan_types = []
# define measurement directories to be processed, and populate the list either with the given include_measurements, or with an intelligent selection
scan_types = deepcopy(functional_scan_types)
scan_types.extend(structural_scan_types)
data_selection=get_data_selection(measurements_base, sessions, scan_types=scan_types, subjects=subjects, exclude_subjects=exclude_subjects, measurements=measurements, exclude_measurements=exclude_measurements)
if not subjects:
subjects = set(list(data_selection["subject"]))
if not sessions:
sessions = set(list(data_selection["session"]))
if structural_registration:
structural_scan_types = [structural_scan_types[0]]
# here we start to define the nipype workflow elements (nodes, connectons, meta)
subjects_sessions = data_selection[["subject","session"]].drop_duplicates().values.tolist()
infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_session']), name="infosource")
infosource.iterables = [('subject_session', subjects_sessions)]
get_f_scan = pe.Node(name='get_f_scan', interface=util.Function(function=get_scan,input_names=inspect.getargspec(get_scan)[0], output_names=['scan_path','scan_type']))
if not strict:
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = data_selection
get_f_scan.inputs.measurements_base = measurements_base
get_f_scan.iterables = ("scan_type", functional_scan_types)
f_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="f_bru2nii")
f_bru2nii.inputs.actual_size=actual_size
dummy_scans = pe.Node(name='dummy_scans', interface=util.Function(function=force_dummy_scans,input_names=inspect.getargspec(force_dummy_scans)[0], output_names=['out_file']))
dummy_scans.inputs.desired_dummy_scans = DUMMY_SCANS
events_file = pe.Node(name='events_file', interface=util.Function(function=write_events_file,input_names=inspect.getargspec(write_events_file)[0], output_names=['out_file']))
events_file.inputs.dummy_scans_ms = DUMMY_SCANS * tr * 1000
events_file.inputs.stim_protocol_dictionary = STIM_PROTOCOL_DICTIONARY
events_file.inputs.very_nasty_bruker_delay_hack = very_nasty_bruker_delay_hack
if realign:
realigner = pe.Node(interface=nipy.SpaceTimeRealigner(), name="realigner")
realigner.inputs.slice_times = "asc_alt_2"
realigner.inputs.tr = tr
realigner.inputs.slice_info = 3 #3 for coronal slices (2 for horizontal, 1 for sagittal)
bandpass = pe.Node(interface=fsl.maths.TemporalFilter(), name="bandpass")
bandpass.inputs.highpass_sigma = highpass_sigma
if lowpass_sigma:
bandpass.inputs.lowpass_sigma = lowpass_sigma
else:
bandpass.inputs.lowpass_sigma = tr
bids_filename = pe.Node(name='bids_filename', interface=util.Function(function=sss_filename,input_names=inspect.getargspec(sss_filename)[0], output_names=['filename']))
bids_stim_filename = pe.Node(name='bids_stim_filename', interface=util.Function(function=sss_filename,input_names=inspect.getargspec(sss_filename)[0], output_names=['filename']))
bids_stim_filename.inputs.suffix = "events"
bids_stim_filename.inputs.extension = ".tsv"
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = path.join(measurements_base,"preprocessing",workflow_name)
datasink.inputs.parameterization = False
workflow_connections = [
(infosource, get_f_scan, [('subject_session', 'selector')]),
(infosource, bids_stim_filename, [('subject_session', 'subject_session')]),
(get_f_scan, bids_stim_filename, [('scan_type', 'scan')]),
(get_f_scan, f_bru2nii, [('scan_path', 'input_dir')]),
(f_bru2nii, dummy_scans, [('nii_file', 'in_file')]),
(get_f_scan, dummy_scans, [('scan_path', 'scan_dir')]),
(get_f_scan, events_file, [
('scan_type', 'scan_type'),
('scan_path', 'scan_dir')
]),
(events_file, datasink, [('out_file', 'func.@events')]),
(bids_stim_filename, events_file, [('filename', 'out_file')]),
(infosource, datasink, [(('subject_session',ss_to_path), 'container')]),
(infosource, bids_filename, [('subject_session', 'subject_session')]),
(get_f_scan, bids_filename, [('scan_type', 'scan')]),
(bids_filename, bandpass, [('filename', 'out_file')]),
(bandpass, datasink, [('out_file', 'func')]),
]
if realign:
workflow_connections.extend([
(dummy_scans, realigner, [('out_file', 'in_file')]),
])
#ADDING SELECTABLE NODES AND EXTENDING WORKFLOW AS APPROPRIATE:
if structural_scan_types:
get_s_scan = pe.Node(name='get_s_scan', interface=util.Function(function=get_scan,input_names=inspect.getargspec(get_scan)[0], output_names=['scan_path','scan_type']))
if not strict:
get_s_scan.inputs.ignore_exception = True
get_s_scan.inputs.data_selection = data_selection
get_s_scan.inputs.measurements_base = measurements_base
get_s_scan.iterables = ("scan_type", structural_scan_types)
s_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="s_bru2nii")
s_bru2nii.inputs.force_conversion=True
s_bru2nii.inputs.actual_size=actual_size
if "DSURQEc" in template:
s_biascorrect = pe.Node(interface=ants.N4BiasFieldCorrection(), name="s_biascorrect")
s_biascorrect.inputs.dimension = 3
s_biascorrect.inputs.bspline_fitting_distance = 10
s_biascorrect.inputs.bspline_order = 4
s_biascorrect.inputs.shrink_factor = 2
s_biascorrect.inputs.n_iterations = [150,100,50,30]
s_biascorrect.inputs.convergence_threshold = 1e-16
s_register, s_warp, _, _ = DSURQEc_structural_registration(template, registration_mask)
#TODO: incl. in func registration
if autorotate:
workflow_connections.extend([
(s_biascorrect, s_rotated, [('output_image', 'out_file')]),
(s_rotated, s_register, [('out_file', 'moving_image')]),
])
else:
workflow_connections.extend([
(s_biascorrect, s_register, [('output_image', 'moving_image')]),
(s_register, s_warp, [('composite_transform', 'transforms')]),
(s_bru2nii, s_warp, [('nii_file', 'input_image')]),
(s_warp, datasink, [('output_image', 'anat')]),
])
else:
s_biascorrect = pe.Node(interface=ants.N4BiasFieldCorrection(), name="s_biascorrect")
s_biascorrect.inputs.dimension = 3
s_biascorrect.inputs.bspline_fitting_distance = 100
s_biascorrect.inputs.shrink_factor = 2
s_biascorrect.inputs.n_iterations = [200,200,200,200]
s_biascorrect.inputs.convergence_threshold = 1e-11
s_reg_biascorrect = pe.Node(interface=ants.N4BiasFieldCorrection(), name="s_reg_biascorrect")
s_reg_biascorrect.inputs.dimension = 3
s_reg_biascorrect.inputs.bspline_fitting_distance = 95
s_reg_biascorrect.inputs.shrink_factor = 2
s_reg_biascorrect.inputs.n_iterations = [500,500,500,500]
s_reg_biascorrect.inputs.convergence_threshold = 1e-14
s_cutoff = pe.Node(interface=fsl.ImageMaths(), name="s_cutoff")
s_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
s_BET = pe.Node(interface=fsl.BET(), name="s_BET")
s_BET.inputs.mask = True
s_BET.inputs.frac = 0.3
s_BET.inputs.robust = True
s_mask = pe.Node(interface=fsl.ApplyMask(), name="s_mask")
s_register, s_warp, _, _ = structural_registration(template)
workflow_connections.extend([
(s_bru2nii, s_reg_biascorrect, [('nii_file', 'input_image')]),
(s_reg_biascorrect, s_cutoff, [('output_image', 'in_file')]),
(s_cutoff, s_BET, [('out_file', 'in_file')]),
(s_biascorrect, s_mask, [('output_image', 'in_file')]),
(s_BET, s_mask, [('mask_file', 'mask_file')]),
])
#TODO: incl. in func registration
if autorotate:
workflow_connections.extend([
(s_mask, s_rotated, [('out_file', 'out_file')]),
(s_rotated, s_register, [('out_file', 'moving_image')]),
])
else:
workflow_connections.extend([
(s_mask, s_register, [('out_file', 'moving_image')]),
(s_register, s_warp, [('composite_transform', 'transforms')]),
(s_bru2nii, s_warp, [('nii_file', 'input_image')]),
(s_warp, datasink, [('output_image', 'anat')]),
])
if(autorotate):
s_rotated = autorotate(template)
s_bids_filename = pe.Node(name='s_bids_filename', interface=util.Function(function=sss_filename,input_names=inspect.getargspec(sss_filename)[0], output_names=['filename']))
s_bids_filename.inputs.scan_prefix = False
workflow_connections.extend([
(infosource, get_s_scan, [('subject_session', 'selector')]),
(infosource, s_bids_filename, [('subject_session', 'subject_session')]),
(get_s_scan, s_bru2nii, [('scan_path','input_dir')]),
(get_s_scan, s_bids_filename, [('scan_type', 'scan')]),
(s_bids_filename, s_warp, [('filename','output_image')]),
(s_bru2nii, s_biascorrect, [('nii_file', 'input_image')]),
])
if functional_registration_method == "structural":
if not structural_scan_types:
raise ValueError('The option `registration="structural"` requires there to be a structural scan type.')
workflow_connections.extend([
(s_register, f_warp, [('composite_transform', 'transforms')]),
])
if realign:
workflow_connections.extend([
(realigner, f_warp, [('out_file', 'input_image')]),
])
else:
workflow_connections.extend([
(dummy_scans, f_warp, [('out_file', 'input_image')]),
])
if functional_registration_method == "composite":
if not structural_scan_types:
raise ValueError('The option `registration="composite"` requires there to be a structural scan type.')
_, _, f_register, f_warp = DSURQEc_structural_registration(template, registration_mask)
temporal_mean = pe.Node(interface=fsl.MeanImage(), name="temporal_mean")
f_biascorrect = pe.Node(interface=ants.N4BiasFieldCorrection(), name="f_biascorrect")
f_biascorrect.inputs.dimension = 3
f_biascorrect.inputs.bspline_fitting_distance = 100
f_biascorrect.inputs.shrink_factor = 2
f_biascorrect.inputs.n_iterations = [200,200,200,200]
f_biascorrect.inputs.convergence_threshold = 1e-11
merge = pe.Node(util.Merge(2), name='merge')
workflow_connections.extend([
(temporal_mean, f_biascorrect, [('out_file', 'input_image')]),
(f_biascorrect, f_register, [('output_image', 'moving_image')]),
(s_biascorrect, f_register, [('output_image', 'fixed_image')]),
(f_register, merge, [('composite_transform', 'in1')]),
(s_register, merge, [('composite_transform', 'in2')]),
(merge, f_warp, [('out', 'transforms')]),
])
if realign:
workflow_connections.extend([
(realigner, temporal_mean, [('out_file', 'in_file')]),
(realigner, f_warp, [('out_file', 'input_image')]),
])
else:
workflow_connections.extend([
(dummy_scans, temporal_mean, [('out_file', 'input_image')]),
(dummy_scans, f_warp, [('out_file', 'input_image')]),
])
elif functional_registration_method == "functional":
f_register, f_warp = functional_registration(template)
temporal_mean = pe.Node(interface=fsl.MeanImage(), name="temporal_mean")
f_biascorrect = pe.Node(interface=ants.N4BiasFieldCorrection(), name="f_biascorrect")
f_biascorrect.inputs.dimension = 3
f_biascorrect.inputs.bspline_fitting_distance = 100
f_biascorrect.inputs.shrink_factor = 2
f_biascorrect.inputs.n_iterations = [200,200,200,200]
f_biascorrect.inputs.convergence_threshold = 1e-11
f_cutoff = pe.Node(interface=fsl.ImageMaths(), name="f_cutoff")
f_cutoff.inputs.op_string = "-thrP 30"
f_BET = pe.Node(interface=fsl.BET(), name="f_BET")
f_BET.inputs.mask = True
f_BET.inputs.frac = 0.5
workflow_connections.extend([
(temporal_mean, f_biascorrect, [('out_file', 'input_image')]),
(f_biascorrect, f_cutoff, [('output_image', 'in_file')]),
(f_cutoff, f_BET, [('out_file', 'in_file')]),
(f_BET, register, [('out_file', 'moving_image')]),
(register, f_warp, [('composite_transform', 'transforms')]),
])
if realign:
workflow_connections.extend([
(realigner, temporal_mean, [('out_file', 'in_file')]),
(realigner, f_warp, [('out_file', 'input_image')]),
])
else:
workflow_connections.extend([
(dummy_scans, temporal_mean, [('out_file', 'input_image')]),
(dummy_scans, f_warp, [('out_file', 'input_image')]),
])
invert = pe.Node(interface=fsl.ImageMaths(), name="invert")
if functional_blur_xy and negative_contrast_agent:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(f_warp, blur, [('output_image', 'in_file')]),
(blur, invert, [(('out_file', fslmaths_invert_values), 'op_string')]),
(blur, invert, [('out_file', 'in_file')]),
(invert, bandpass, [('out_file', 'in_file')]),
])
elif functional_blur_xy:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(f_warp, blur, [('output_image', 'in_file')]),
(blur, bandpass, [('out_file', 'in_file')]),
])
elif negative_contrast_agent:
blur = pe.Node(interface=afni.preprocess.BlurToFWHM(), name="blur")
blur.inputs.fwhmxy = functional_blur_xy
workflow_connections.extend([
(f_warp, invert, [(('output_image', fslmaths_invert_values), 'op_string')]),
(f_warp, invert, [('output_image', 'in_file')]),
(invert, bandpass, [('out_file', 'in_file')]),
])
else:
workflow_connections.extend([
(f_warp, bandpass, [('output_image', 'in_file')]),
])
workdir_name = workflow_name+"_work"
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(measurements_base,"preprocessing")
workflow.config = {"execution": {"crashdump_dir": path.join(measurements_base,"preprocessing/crashdump")}}
workflow.write_graph(dotfilename=path.join(workflow.base_dir,workdir_name,"graph.dot"), graph2use="hierarchical", format="png")
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir,workdir_name))
def metadata():
from samri.pipelines.extra_functions import get_data_selection
info = get_data_selection('~/ni_data/test')
print(info)
def bru2bids(measurements_base,
measurements=[],
inflated_size=False,
bids_extra=['acq','run'],
dataset_name=False,
debug=False,
diffusion_match={},
exclude={},
functional_match={},
keep_crashdump=False,
keep_work=False,
n_procs=N_PROCS,
out_base=None,
structural_match={},
workflow_name='bids',
):
"""
Convert and reorganize Bruker "raw" directories (2dseq and ParaVision-formatted metadata files) into a BIDS-organized file hierarchy containing NIfTI files and associated metadata.
If any exist, this workflow also reposits COSplay event files (already written according to BIDS) in the correct place in the output hierarchy.
Parameters
----------
measurements_base : str
Path of the top level directory containing all the Bruker scan directories to be converted and reformatted.
bids_extra : list, optional
List of strings denoting optional BIDS fields to include in the resulting file names.
Accepted items are 'acq' and 'run'.
inflated_size : bool, optional
Whether to inflate the voxel size reported by the scanner when converting the data to NIfTI.
Setting this to `True` multiplies the voxel edge lengths by 10 (i.e. the volume by 1000); this is occasionally done in some small animal pipelines, which use routines designed exclusively for human data.
Unless you are looking to reproduce such a workflow, this should be set to `True`.
dataset_name : string, optional
A dataset name that will be written into the BIDS metadata file.
Generally not needed, as by default we use the dataset path to satisfy this BIDS requirement.
debug : bool, optional
Whether to enable debug support.
This prints the data selection before passing it to the nipype workflow management system, and turns on debug support in nipype (leading to more verbose logging).
diffusion_match : dict, optional
A dictionary with any combination of "session", "subject", "task", and "acquisition" as keys and corresponding lists of identifiers as values.
Only diffusion scans matching all identifiers will be included - i.e. this is a whitelist.
exclude : dict, optional
A dictionary with any combination of "session", "subject", "task" , and "acquisition" as keys and corresponding identifiers as values.
Only scans not matching any of the listed criteria will be included in the workfolow - i.e. this is a blacklist (for functional and structural scans).
functional_match : dict, optional
A dictionary with any combination of "session", "subject", "task", and "acquisition" as keys and corresponding lists of identifiers as values.
Only Functional scans matching all identifiers will be included - i.e. this is a whitelist.
keep_work : bool, optional
Whether to keep the work directory (containing all the intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
keep_crashdump : bool, optional
Whether to keep the crashdump directory (containing all the crash reports for intermediary workflow steps, as managed by nipypye).
This is useful for debugging and quality control.
n_procs : int, optional
Maximum number of processes which to simultaneously spawn for the workflow.
If not explicitly defined, this is automatically calculated from the number of available cores and under the assumption that the workflow will be the main process running for the duration that it is running.
out_base : str, optional
Base directory in which to place the BIDS reposited data.
If not present the BIDS records will be created in the `measurements_base` directory.
structural_match : dict, optional
A dictionary with any combination of "session", "subject", "task", and "acquisition" as keys and corresponding lists of identifiers as values.
Only structural scans matching all identifiers will be included - i.e. this is a whitelist.
workflow_name : str, optional
Top level name for the output directory.
"""
measurements_base = path.abspath(path.expanduser(measurements_base))
if out_base:
out_base = path.abspath(path.expanduser(out_base))
else:
out_base = measurements_base
out_dir = path.join(out_base,workflow_name)
workdir_name = workflow_name+'_work'
workdir = path.join(out_base,workdir_name)
# define measurement directories to be processed, and populate the list either with the given include_measurements, or with an intelligent selection
functional_scan_types = diffusion_scan_types = structural_scan_types = []
data_selection = pd.DataFrame([])
if structural_match:
s_data_selection = get_data_selection(measurements_base,
match=structural_match,
exclude=exclude,
measurements=measurements,
)
structural_scan_types = list(s_data_selection['scan_type'].unique())
struct_ind = s_data_selection.index.tolist()
data_selection = pd.concat([data_selection,s_data_selection], sort=True)
if functional_match:
f_data_selection = get_data_selection(measurements_base,
match=functional_match,
exclude=exclude,
measurements=measurements,
)
functional_scan_types = list(f_data_selection['scan_type'].unique())
func_ind = f_data_selection.index.tolist()
data_selection = pd.concat([data_selection,f_data_selection], sort=True)
if diffusion_match:
d_data_selection = get_data_selection(measurements_base,
match=diffusion_match,
exclude=exclude,
measurements=measurements,
)
diffusion_scan_types = list(d_data_selection['scan_type'].unique())
dwi_ind = d_data_selection.index.tolist()
data_selection = pd.concat([data_selection,d_data_selection], sort=True)
# we start to define nipype workflow elements (nodes, connections, meta)
subjects_sessions = data_selection[["subject","session"]].drop_duplicates().values.tolist()
if debug:
print('Data selection:')
print(data_selection)
print('Iterating over:')
print(subjects_sessions)
infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_session'], mandatory_inputs=False), name="infosource")
infosource.iterables = [('subject_session', subjects_sessions)]
datasink = pe.Node(nio.DataSink(), name='datasink')
datasink.inputs.base_directory = out_dir
datasink.inputs.parameterization = False
workflow_connections = [
(infosource, datasink, [(('subject_session',ss_to_path), 'container')]),
]
if functional_scan_types:
if not os.path.exists(workdir):
os.makedirs(workdir)
f_data_selection.to_csv(path.join(workdir,'f_data_selection.csv'))
get_f_scan = pe.Node(name='get_f_scan', interface=util.Function(function=get_bids_scan,input_names=inspect.getargspec(get_bids_scan)[0], output_names=[
'scan_path', 'typ', 'task', 'nii_path', 'nii_name', 'eventfile_name', 'subject_session', 'metadata_filename', 'dict_slice',
]))
get_f_scan.inputs.ignore_exception = True
get_f_scan.inputs.data_selection = f_data_selection
get_f_scan.inputs.bids_base = measurements_base
get_f_scan.iterables = ("ind_type", func_ind)
f_bru2nii = pe.Node(interface=Bru2(), name="f_bru2nii")
f_bru2nii.inputs.actual_size = not inflated_size
f_bru2nii.inputs.compress = True
f_metadata_file = pe.Node(name='metadata_file', interface=util.Function(function=write_bids_metadata_file,input_names=inspect.getargspec(write_bids_metadata_file)[0], output_names=['out_file']))
f_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
events_file = pe.Node(name='events_file', interface=util.Function(function=write_bids_events_file,input_names=inspect.getargspec(write_bids_events_file)[0], output_names=['out_file']))
events_file.ignore_exception = True
workflow_connections = [
(get_f_scan, datasink, [(('subject_session',ss_to_path), 'container')]),
(get_f_scan, f_bru2nii, [('scan_path', 'input_dir')]),
(get_f_scan, f_bru2nii, [('nii_name', 'output_filename')]),
(f_metadata_file, events_file, [('out_file', 'metadata_file')]),
(f_bru2nii, events_file, [('nii_file', 'timecourse_file')]),
(f_bru2nii, datasink, [('nii_file', 'func')]),
(get_f_scan, f_metadata_file, [
('metadata_filename', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')
]),
(get_f_scan, events_file, [
('eventfile_name', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')
]),
(events_file, datasink, [('out_file', 'func.@events')]),
(f_metadata_file, datasink, [('out_file', 'func.@metadata')]),
]
crashdump_dir = path.join(out_base,workflow_name+'_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level':'DEBUG',
'utils_level':'DEBUG',
'interface_level':'DEBUG',
'filemanip_level':'DEBUG',
'log_to_file':'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(out_base)
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,workdir_name,"graph_structural.dot"), graph2use="hierarchical", format="png")
except OSError:
print('We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.')
#Execute the workflow
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir,workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except (FileNotFoundError, OSError):
pass
if diffusion_scan_types:
# We check for the directory, since it gets deleted after a successful execution.
if not os.path.exists(workdir):
os.makedirs(workdir)
d_data_selection.to_csv(path.join(workdir,'d_data_selection.csv'))
get_d_scan = pe.Node(name='get_d_scan', interface=util.Function(function=get_bids_scan,input_names=inspect.getargspec(get_bids_scan)[0], output_names=[
'scan_path', 'typ', 'task', 'nii_path', 'nii_name', 'eventfile_name', 'subject_session', 'metadata_filename', 'dict_slice',
]))
get_d_scan.inputs.ignore_exception = True
get_d_scan.inputs.data_selection = d_data_selection
get_d_scan.inputs.extra = ['acq']
get_d_scan.inputs.bids_base = measurements_base
get_d_scan.iterables = ("ind_type", dwi_ind)
d_bru2nii = pe.Node(interface=Bru2(), name="d_bru2nii")
d_bru2nii.inputs.force_conversion=True
d_bru2nii.inputs.actual_size = not inflated_size
d_bru2nii.inputs.compress = True
d_metadata_file = pe.Node(name='metadata_file', interface=util.Function(function=write_bids_metadata_file,input_names=inspect.getargspec(write_bids_metadata_file)[0], output_names=['out_file']))
d_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
workflow_connections = [
(get_d_scan, datasink, [(('subject_session',ss_to_path), 'container')]),
(get_d_scan, d_bru2nii, [('scan_path', 'input_dir')]),
(get_d_scan, d_bru2nii, [('nii_name', 'output_filename')]),
(d_bru2nii, datasink, [('nii_file', 'dwi')]),
(get_d_scan, d_metadata_file, [
('metadata_filename', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')
]),
(d_metadata_file, datasink, [('out_file', 'dwi.@metadata')]),
]
crashdump_dir = path.join(out_base,workflow_name+'_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level':'DEBUG',
'utils_level':'DEBUG',
'interface_level':'DEBUG',
'filemanip_level':'DEBUG',
'log_to_file':'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(out_base)
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,workdir_name,"graph_diffusion.dot"), graph2use="hierarchical", format="png")
except OSError:
print('We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.')
#Execute the workflow
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir,workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except (FileNotFoundError, OSError):
pass
if structural_scan_types:
# We check for the directory, since it gets deleted after a successful execution.
if not os.path.exists(workdir):
os.makedirs(workdir)
s_data_selection.to_csv(path.join(workdir,'s_data_selection.csv'))
get_s_scan = pe.Node(name='get_s_scan', interface=util.Function(function=get_bids_scan,input_names=inspect.getargspec(get_bids_scan)[0], output_names=[
'scan_path', 'typ', 'task', 'nii_path', 'nii_name', 'eventfile_name', 'subject_session', 'metadata_filename', 'dict_slice',
]))
get_s_scan.inputs.ignore_exception = True
get_s_scan.inputs.data_selection = s_data_selection
get_s_scan.inputs.extra = ['acq']
get_s_scan.inputs.bids_base = measurements_base
get_s_scan.iterables = ("ind_type", struct_ind)
s_bru2nii = pe.Node(interface=Bru2(), name="s_bru2nii")
s_bru2nii.inputs.force_conversion=True
s_bru2nii.inputs.actual_size = not inflated_size
s_bru2nii.inputs.compress = True
s_metadata_file = pe.Node(name='metadata_file', interface=util.Function(function=write_bids_metadata_file,input_names=inspect.getargspec(write_bids_metadata_file)[0], output_names=['out_file']))
s_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
workflow_connections = [
(get_s_scan, datasink, [(('subject_session',ss_to_path), 'container')]),
(get_s_scan, s_bru2nii, [('scan_path', 'input_dir')]),
(get_s_scan, s_bru2nii, [('nii_name', 'output_filename')]),
(s_bru2nii, datasink, [('nii_file', 'anat')]),
(get_s_scan, s_metadata_file, [
('metadata_filename', 'out_file'),
('task', 'task'),
('scan_path', 'scan_dir')
]),
(s_metadata_file, datasink, [('out_file', 'anat.@metadata')]),
]
crashdump_dir = path.join(out_base,workflow_name+'_crashdump')
workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
if debug:
workflow_config['logging'] = {
'workflow_level':'DEBUG',
'utils_level':'DEBUG',
'interface_level':'DEBUG',
'filemanip_level':'DEBUG',
'log_to_file':'true',
}
workflow = pe.Workflow(name=workdir_name)
workflow.connect(workflow_connections)
workflow.base_dir = path.join(out_base)
workflow.config = workflow_config
try:
workflow.write_graph(dotfilename=path.join(workflow.base_dir,workdir_name,"graph_structural.dot"), graph2use="hierarchical", format="png")
except OSError:
print('We could not write the DOT file for visualization (`dot` function from the graphviz package). This is non-critical to the processing, but you should get this fixed.')
#Execute the workflow
if not keep_work or not keep_crashdump:
try:
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
except RuntimeError:
pass
else:
workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
if not keep_work:
shutil.rmtree(path.join(workflow.base_dir,workdir_name))
if not keep_crashdump:
try:
shutil.rmtree(crashdump_dir)
except (FileNotFoundError, OSError):
pass
# This is needed because BIDS does not yet support CBV
with open(path.join(out_dir,".bidsignore"), "w+") as f:
f.write('*_cbv.*')
# Create essions files
sessions_file(out_dir, data_selection)
# BIDS needs a descriptor file
if not dataset_name:
dataset_name = measurements_base
description = {
'Name':dataset_name,
'BIDSVersion':'1.0.2',
}
with open(path.join(out_dir,'dataset_description.json'), 'w') as f:
json.dump(description, f)