def __init__(self, in_file='path', **options):
from nipype.interfaces.fsl import ImageMaths
fslmaths = ImageMaths()
fslmaths.inputs.in_file = in_file
for ef in options:
setattr(fslmaths.inputs, ef, options[ef])
self.res = fslmaths.run()
def init_b1_mcf(rf_pulse=None, scale=150):
inputnode = Node(IdentityInterface(fields=['2db1map_file', 'ref_file']),
name='inputnode')
outputnode = Node(IdentityInterface(fields=['b1_plus', 'b1_pulse']),
name='outputnode')
b1_b1 = Node(ExtractROI(t_min=0, t_size=1), name='b1_extract_b1')
b1_filter = Node(Filter(filter_spec='Gauss,3.0'), name='b1_filter')
b1_mag = Node(ExtractROI(t_min=1, t_size=1), name='b1_extract_mag')
b1_reg = Node(FLIRT(out_file='b1mag_reg.nii.gz',
out_matrix_file='b1mag_reg.mat'),
name='b1_reg')
b1_invert = Node(ConvertXFM(invert_xfm=True), name='b1_invert')
b1_apply = Node(FLIRT(apply_xfm=True), name='b1_reg_apply')
b1_scale = Node(ImageMaths(op_string='-div %f' % scale), name='b1_scale')
wf = Workflow(name='b1_prep')
wf.connect([(inputnode, b1_b1, [('2db1map_file', 'in_file')]),
(inputnode, b1_mag, [('2db1map_file', 'in_file')]),
(inputnode, b1_reg, [('ref_file', 'in_file')]),
(inputnode, b1_apply, [('ref_file', 'reference')]),
(b1_mag, b1_reg, [('roi_file', 'reference')]),
(b1_reg, b1_invert, [('out_matrix_file', 'in_file')]),
(b1_invert, b1_apply, [('out_file', 'in_matrix_file')]),
(b1_b1, b1_filter, [('roi_file', 'in_file')]),
(b1_filter, b1_apply, [('out_file', 'in_file')]),
(b1_apply, b1_scale, [('out_file', 'in_file')]),
(b1_scale, outputnode, [('out_file', 'b1_plus')])])
if rf_pulse:
b1_rf = Node(RFProfile(rf=rf_pulse, out_file='b1_rf.nii.gz'),
name='b1_rf')
wf.connect([(b1_scale, b1_rf, [('out_file', 'in_file')]),
(b1_rf, outputnode, [('out_file', 'b1_pulse')])])
return wf
def cert(zfrqs):
inputnode = Node(IdentityInterface(fields=['cert_180', 'cert_360', 'mask_file']),
name='inputnode')
outputnode = Node(IdentityInterface(fields=['cert_spectrum', 'cert_amide']),
name='outputnode')
cert_sub = Node(ImageMaths(op_string='-sub', out_file='cert.nii.gz'),
name='cert_subtract', iterfield=['in_file'])
amide_index = (np.abs(zfrqs - 3.5)).argmin()
amide = Node(Select(volumes=[amide_index], out_file='amide.nii.gz'),
name='select_amide')
cert = Workflow(name='CERT')
cert.connect([(inputnode, cert_sub, [('cert_360', 'in_file'), ('cert_180', 'in_file2')]),
(cert_sub, amide, [('out_file', 'in_file')]),
(cert_sub, outputnode, [('out_file', 'cert_spectrum')]),
(amide, outputnode, [('out_file', 'cert_amide')])
])
return cert
def cert(zfrqs):
inputnode = Node(IdentityInterface(fields=['cert_180', 'cert_360', 'mask_file']),
name='inputnode')
outputnode = Node(IdentityInterface(fields=['cert_spectrum', 'cert_amide']),
name='outputnode')
cert_sub = Node(ImageMaths(op_string='-sub', out_file='cert.nii.gz'),
name='cert_subtract')
amide_index = (np.abs(zfrqs - 3.5)).argmin()
amide = Node(ExtractROI(t_min=amide_index, t_size=1),
name='amide_extract')
cert = Workflow(name='CERT')
cert.connect([(inputnode, cert_sub, [('cert_360', 'in_file'), ('cert_180', 'in_file2')]),
(cert_sub, amide, [('out_file', 'in_file')]),
(cert_sub, outputnode, [('out_file', 'cert_spectrum')]),
(amide, outputnode, [('roi_file', 'cert_amide')])
])
return cert
def create_subject_ffx_wf(
sub_id, bet_fracthr, spatial_fwhm, susan_brightthresh, hp_vols,
lp_vols, remove_hemi, film_thresh, film_model_autocorr, use_derivs, tr,
tcon_subtractive, cluster_threshold, cluster_thresh_frac, cluster_p,
dilate_clusters_voxel, cond_ids, dsdir, work_basedir):
# todo: new mapnode inputs: cluster_threshold, cluster_p
"""
Make a workflow including preprocessing, first level, and second level GLM analysis for a given subject.
This pipeline includes:
- skull stripping
- spatial smoothing
- removing the irrelevant hemisphere
- temporal band pass filter
- 1st level GLM
- averaging f-contrasts from 1st level GLM
- clustering run-wise f-tests, dilating clusters, and returning binary roi mask
"""
from nipype.algorithms.modelgen import SpecifyModel
from nipype.interfaces.fsl import BET, SUSAN, ImageMaths
from nipype.interfaces.fsl.model import SmoothEstimate, Cluster
from nipype.interfaces.fsl.maths import TemporalFilter, MathsCommand
from nipype.interfaces.utility import Function
from nipype.pipeline.engine import Workflow, Node, MapNode
from nipype.workflows.fmri.fsl import create_modelfit_workflow
from nipype.interfaces.fsl.maths import MultiImageMaths
from nipype.interfaces.utility import IdentityInterface
import sys
from os.path import join as pjoin
import os
sys.path.insert(
0, "/data/project/somato/raw/code/roi_glm/custom_node_functions.py")
# TODO: don't hardcode this
import custom_node_functions
# set up sub-workflow
sub_wf = Workflow(name='subject_%s_wf' % sub_id)
# set up sub-working-directory
subwf_wd = pjoin(work_basedir, 'subject_ffx_wfs',
'subject_%s_ffx_workdir' % sub_id)
if not os.path.exists(subwf_wd):
os.makedirs(subwf_wd)
sub_wf.base_dir = subwf_wd
# Grab bold files for all four runs of one subject.
# in the order [d1_d5, d5_d1, blocked_design1, blocked_design2]
grab_boldfiles = Node(Function(
function=custom_node_functions.grab_boldfiles_subject,
input_names=['sub_id', 'cond_ids', 'ds_dir'],
output_names=['boldfiles']),
name='grab_boldfiles')
grab_boldfiles.inputs.sub_id = sub_id
grab_boldfiles.inputs.cond_ids = cond_ids
grab_boldfiles.inputs.ds_dir = dsdir
getonsets = Node(Function(
function=custom_node_functions.grab_blocked_design_onsets_subject,
input_names=['sub_id', 'prepped_ds_dir'],
output_names=['blocked_design_onsets_dicts']),
name='getonsets')
getonsets.inputs.sub_id = sub_id
getonsets.inputs.prepped_ds_dir = dsdir
# pass bold files through preprocessing pipeline
bet = MapNode(BET(frac=bet_fracthr, functional=True, mask=True),
iterfield=['in_file'],
name='bet')
pick_mask = Node(Function(function=custom_node_functions.pick_first_mask,
input_names=['mask_files'],
output_names=['first_mask']),
name='pick_mask')
# SUSAN smoothing node
susan = MapNode(SUSAN(fwhm=spatial_fwhm,
brightness_threshold=susan_brightthresh),
iterfield=['in_file'],
name='susan')
# bandpass filter node
bpf = MapNode(TemporalFilter(highpass_sigma=hp_vols / 2.3548,
lowpass_sigma=lp_vols / 2.3548),
iterfield=['in_file'],
name='bpf')
# cut away hemisphere node
if remove_hemi == 'r':
roi_args = '-roi 96 -1 0 -1 0 -1 0 -1'
elif remove_hemi == 'l':
roi_args = '-roi 0 96 0 -1 0 -1 0 -1'
else:
raise IOError('did not recognite value of remove_hemi %s' %
remove_hemi)
cut_hemi_func = MapNode(MathsCommand(),
iterfield=['in_file'],
name='cut_hemi_func')
cut_hemi_func.inputs.args = roi_args
cut_hemi_mask = MapNode(MathsCommand(),
iterfield=['in_file'],
name='cut_hemi_mask')
cut_hemi_mask.inputs.args = roi_args
# Make Design and Contrasts for that subject
# subject_info ist a list of two "Bunches", each for one run, containing conditions, onsets, durations
designgen = Node(Function(
input_names=['subtractive_contrast', 'blocked_design_onsets_dicts'],
output_names=['subject_info', 'contrasts'],
function=custom_node_functions.make_bunch_and_contrasts),
name='designgen')
designgen.inputs.subtractive_contrasts = tcon_subtractive
# create 'session_info' for modelfit
modelspec = MapNode(SpecifyModel(input_units='secs'),
name='modelspec',
iterfield=['functional_runs', 'subject_info'])
modelspec.inputs.high_pass_filter_cutoff = hp_vols * tr
modelspec.inputs.time_repetition = tr
flatten_session_infos = Node(Function(
input_names=['nested_list'],
output_names=['flat_list'],
function=custom_node_functions.flatten_nested_list),
name='flatten_session_infos')
# Fist-level workflow
modelfit = create_modelfit_workflow(f_contrasts=True)
modelfit.inputs.inputspec.interscan_interval = tr
modelfit.inputs.inputspec.film_threshold = film_thresh
modelfit.inputs.inputspec.model_serial_correlations = film_model_autocorr
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': use_derivs}}
# node that reshapes list of copes returned from modelfit
cope_sorter = Node(Function(input_names=['copes', 'varcopes', 'contrasts'],
output_names=['copes', 'varcopes', 'n_runs'],
function=custom_node_functions.sort_copes),
name='cope_sorter')
# average zfstats from both runs
split_zfstats = Node(Function(
function=custom_node_functions.split_zfstats_runs,
input_names=['zfstats_list'],
output_names=['zfstat_run1', 'zfstat_run2']),
name='split_zfstats')
average_zfstats = Node(MultiImageMaths(op_string='-add %s -div 2'),
name='mean_images')
# estimate smoothness of 1st lvl zf-files
smoothest = MapNode(SmoothEstimate(),
name='smoothest',
iterfield=['mask_file', 'zstat_file'])
cluster = MapNode(Cluster(),
name='cluster',
iterfield=['in_file', 'volume', 'dlh'])
cluster.inputs.threshold = cluster_threshold
cluster.inputs.pthreshold = cluster_p
cluster.inputs.fractional = cluster_thresh_frac
cluster.inputs.no_table = True
cluster.inputs.out_threshold_file = True
cluster.inputs.out_pval_file = True
cluster.inputs.out_localmax_vol_file = True
cluster.inputs.out_max_file = True
cluster.inputs.out_size_file = True
# dilate clusters
dilate = MapNode(MathsCommand(args='-kernel sphere %i -dilD' %
dilate_clusters_voxel),
iterfield=['in_file'],
name='dilate')
# binarize the result to a mask
binarize_roi = MapNode(ImageMaths(op_string='-nan -thr 0.001 -bin'),
iterfield=['in_file'],
name='binarize_roi')
# connect preprocessing
sub_wf.connect(grab_boldfiles, 'boldfiles', bet, 'in_file')
sub_wf.connect(bet, 'out_file', susan, 'in_file')
sub_wf.connect(susan, 'smoothed_file', bpf, 'in_file')
sub_wf.connect(bpf, 'out_file', cut_hemi_func, 'in_file')
sub_wf.connect(bet, 'mask_file', cut_hemi_mask, 'in_file')
# connect to 1st level model
sub_wf.connect(cut_hemi_func, 'out_file', modelspec, 'functional_runs')
sub_wf.connect(getonsets, 'blocked_design_onsets_dicts', designgen,
'blocked_design_onsets_dicts')
sub_wf.connect(designgen, 'subject_info', modelspec, 'subject_info')
sub_wf.connect(modelspec, 'session_info', flatten_session_infos,
'nested_list')
sub_wf.connect(flatten_session_infos, 'flat_list', modelfit,
'inputspec.session_info')
sub_wf.connect(designgen, 'contrasts', modelfit, 'inputspec.contrasts')
sub_wf.connect(cut_hemi_func, 'out_file', modelfit,
'inputspec.functional_data')
# connect to cluster thresholding
sub_wf.connect(cut_hemi_mask, 'out_file', smoothest, 'mask_file')
sub_wf.connect(modelfit.get_node('modelestimate'), 'zfstats', smoothest,
'zstat_file')
sub_wf.connect(modelfit.get_node('modelestimate'), 'zfstats', cluster,
'in_file')
sub_wf.connect(smoothest, 'dlh', cluster, 'dlh')
sub_wf.connect(smoothest, 'volume', cluster, 'volume')
sub_wf.connect(cluster, 'threshold_file', dilate, 'in_file')
sub_wf.connect(dilate, 'out_file', binarize_roi, 'in_file')
# connect to averaging f-contrasts
sub_wf.connect(modelfit.get_node('modelestimate'), 'zfstats',
split_zfstats, 'zfstats_list')
sub_wf.connect(split_zfstats, 'zfstat_run1', average_zfstats, 'in_file')
sub_wf.connect(split_zfstats, 'zfstat_run2', average_zfstats,
'operand_files')
# redirect to outputspec
# TODO: redirekt outputspec to datasink in meta-wf
outputspec = Node(IdentityInterface(fields=[
'threshold_file', 'index_file', 'pval_file', 'localmax_txt_file'
]),
name='outputspec')
sub_wf.connect(cluster, 'threshold_file', outputspec, 'threshold_file')
sub_wf.connect(cluster, 'index_file', outputspec, 'index_file')
sub_wf.connect(cluster, 'pval_file', outputspec, 'pval_file')
sub_wf.connect(cluster, 'localmax_txt_file', outputspec,
'localmax_txt_file')
sub_wf.connect(binarize_roi, 'out_file', outputspec, 'roi')
# run subject-lvl workflow
# sub_wf.write_graph(graph2use='colored', dotfilename='./subwf_graph.dot')
# sub_wf.run(plugin='MultiProc', plugin_args={'n_procs': 6})
# sub_wf.run(plugin='CondorDAGMan')
# sub_wf.run()
return sub_wf
def structural_to_functional_per_participant_test(subjects_sessions,
template = "~/GitHub/mriPipeline/templates/waxholm/new/WHS_SD_masked.nii.gz",
f_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
num_threads = 3,
):
template = os.path.expanduser(template)
for subject_session in subjects_sessions:
func_image_dir = os.path.expanduser(f_file_format.format(**subject_session))
struct_image_dir = os.path.expanduser(s_file_format.format(**subject_session))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir,myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir,myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200,200,200,200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}_{}_1_biasCorrection_forRegistration.nii.gz'.format(*subject_session.values())
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500,500,500,500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}_{}_1_biasCorrection_forMasking.nii.gz'.format(*subject_session.values())
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET.inputs.out_file = '{}_{}_2_brainExtraction.nii.gz'.format(*subject_session.values())
struct_BET_res = struct_BET.run()
# we need/can not apply a fill, because the "holes" if any, will be at the rostral edge (touching it, and thus not counting as holes)
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask.inputs.out_file = '{}_{}_3_brainMasked.nii.gz'.format(*subject_session.values())
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0,), (1.0, 3.0, 5.0)] ##
struct_registration.inputs.number_of_iterations = [[2000, 1000, 500], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11, 1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1], [4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1],[3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [True, True]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = num_threads
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}_{}_4_structuralRegistration.nii.gz'.format(*subject_session.values())
struct_registration_res = struct_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}_{}_5_functionalWarp.nii.gz'.format(*subject_session.values())
warp.num_threads = num_threads
warp.inputs.input_image = func_image
warp.inputs.transforms = struct_registration_res.outputs.composite_transform
warp.run()
def main(paths, options_binary_string, ANAT, num_proc=7):
json_path = paths[0]
base_directory = paths[1]
motion_correction_bet_directory = paths[2]
parent_wf_directory = paths[3]
# functional_connectivity_directory=paths[4]
coreg_reg_directory = paths[5]
atlas_resize_reg_directory = paths[6]
subject_list = paths[7]
datasink_name = paths[8]
# fc_datasink_name=paths[9]
atlasPath = paths[10]
# brain_path=paths[11]
# mask_path=paths[12]
# atlas_path=paths[13]
# tr_path=paths[14]
# motion_params_path=paths[15]
# func2std_mat_path=paths[16]
# MNI3mm_path=paths[17]
# demographics_file_path = paths[18]
# phenotype_file_path = paths[19]
data_directory = paths[20]
number_of_subjects = len(subject_list)
print("Working with ", number_of_subjects, " subjects.")
# Create our own custom function - BIDSDataGrabber using a Function Interface.
# In[858]:
def get_nifti_filenames(subject_id, data_dir):
# Remember that all the necesary imports need to be INSIDE the function for the Function Interface to work!
from bids.grabbids import BIDSLayout
layout = BIDSLayout(data_dir)
run = 1
anat_file_path = [
f.filename for f in layout.get(
subject=subject_id, type='T1w', extensions=['nii', 'nii.gz'])
]
func_file_path = [
f.filename for f in layout.get(subject=subject_id,
type='bold',
run=run,
extensions=['nii', 'nii.gz'])
]
if len(anat_file_path) == 0:
return None, func_file_path[0] # No Anatomical files present
return anat_file_path[0], func_file_path[0]
BIDSDataGrabber = Node(Function(
function=get_nifti_filenames,
input_names=['subject_id', 'data_dir'],
output_names=['anat_file_path', 'func_file_path']),
name='BIDSDataGrabber')
# BIDSDataGrabber.iterables = [('subject_id',subject_list)]
BIDSDataGrabber.inputs.data_dir = data_directory
# ## Return TR
def get_TR(in_file):
from bids.grabbids import BIDSLayout
data_directory = '/home1/varunk/data/ABIDE1/RawDataBIDs'
layout = BIDSLayout(data_directory)
metadata = layout.get_metadata(path=in_file)
TR = metadata['RepetitionTime']
return TR
# ---------------- Added new Node to return TR and other slice timing correction params-------------------------------
def _getMetadata(in_file):
from bids.grabbids import BIDSLayout
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.DEBUG)
# create a file handler
handler = logging.FileHandler('progress.log')
# add the handlers to the logger
logger.addHandler(handler)
interleaved = True
index_dir = False
data_directory = '/home1/varunk/data/ABIDE1/RawDataBIDs'
layout = BIDSLayout(data_directory)
metadata = layout.get_metadata(path=in_file)
print(metadata)
logger.info('Extracting Meta Data of file: %s', in_file)
try:
tr = metadata['RepetitionTime']
except KeyError:
print(
'Key RepetitionTime not found in task-rest_bold.json so using a default of 2.0 '
)
tr = 2
logger.error(
'Key RepetitionTime not found in task-rest_bold.json for file %s so using a default of 2.0 ',
in_file)
try:
slice_order = metadata['SliceAcquisitionOrder']
except KeyError:
print(
'Key SliceAcquisitionOrder not found in task-rest_bold.json so using a default of interleaved ascending '
)
logger.error(
'Key SliceAcquisitionOrder not found in task-rest_bold.json for file %s so using a default of interleaved ascending',
in_file)
return tr, index_dir, interleaved
if slice_order.split(' ')[0] == 'Sequential':
interleaved = False
if slice_order.split(' ')[1] == 'Descending':
index_dir = True
return tr, index_dir, interleaved
getMetadata = Node(Function(
function=_getMetadata,
input_names=['in_file'],
output_names=['tr', 'index_dir', 'interleaved']),
name='getMetadata')
# ### Skipping 4 starting scans
# Extract ROI for skipping first 4 scans of the functional data
# > **Arguments:**
# t_min: (corresponds to time dimension) Denotes the starting time of the inclusion
# t_size: Denotes the number of scans to include
#
# The logic behind skipping 4 initial scans is to take scans after the subject has stabalized in the scanner.
# In[863]:
# ExtractROI - skip dummy scans
extract = Node(ExtractROI(t_min=4, t_size=-1),
output_type='NIFTI',
name="extract")
# ### Slice time correction
# Created a Node that does slice time correction
# > **Arguments**:
# index_dir=False -> Slices were taken bottom to top i.e. in ascending order
# interleaved=True means odd slices were acquired first and then even slices [or vice versa(Not sure)]
slicetimer = Node(SliceTimer(output_type='NIFTI'), name="slicetimer")
# ### Motion Correction
# Motion correction is done using fsl's mcflirt. It alligns all the volumes of a functional scan to each other
# MCFLIRT - motion correction
mcflirt = Node(MCFLIRT(mean_vol=True, save_plots=True,
output_type='NIFTI'),
name="mcflirt")
# Just a dummy node to transfer the output of Mcflirt to the next workflow. Needed if we didnt want to use the Mcflirt
from_mcflirt = Node(IdentityInterface(fields=['in_file']),
name="from_mcflirt")
# ### Skull striping
# I used fsl's BET
# In[868]:
skullStrip = Node(BET(mask=False, frac=0.3, robust=True),
name='skullStrip') #
# *Note*: Do not include special characters in ```name``` field above coz then wf.writegraph will cause issues
# ## Resample
# I needed to resample the anatomical file from 1mm to 3mm. Because registering a 1mm file was taking a huge amount of time.
#
# In[872]:
# Resample - resample anatomy to 3x3x3 voxel resolution
resample_mni = Node(
Resample(
voxel_size=(3, 3, 3),
resample_mode='Cu', # cubic interpolation
outputtype='NIFTI'),
name="resample_mni")
resample_anat = Node(
Resample(
voxel_size=(3, 3, 3),
resample_mode='Cu', # cubic interpolation
outputtype='NIFTI'),
name="resample_anat")
# In[873]:
resample_atlas = Node(
Resample(
voxel_size=(3, 3, 3),
resample_mode='NN', # cubic interpolation
outputtype='NIFTI'),
name="resample_atlas")
resample_atlas.inputs.in_file = atlasPath
# # Matrix operations
# ### For concatenating the transformation matrices
concat_xform = Node(ConvertXFM(concat_xfm=True), name='concat_xform')
# Node to calculate the inverse of func2std matrix
inv_mat = Node(ConvertXFM(invert_xfm=True), name='inv_mat')
# ## Extracting the mean brain
meanfunc = Node(interface=ImageMaths(op_string='-Tmean', suffix='_mean'),
name='meanfunc')
meanfuncmask = Node(interface=BET(mask=True, no_output=True, frac=0.3),
name='meanfuncmask')
# ## Apply Mask
# Does BET (masking) on the whole func scan [Not using this, creates bug for join node]
maskfunc = Node(interface=ImageMaths(suffix='_bet', op_string='-mas'),
name='maskfunc')
# Does BET (masking) on the mean func scan
maskfunc4mean = Node(interface=ImageMaths(suffix='_bet', op_string='-mas'),
name='maskfunc4mean')
# ## Datasink
# I needed to define the structure of what files are saved and where.
# Create DataSink object
dataSink = Node(DataSink(), name='datasink')
# Name of the output folder
dataSink.inputs.base_directory = opj(base_directory, datasink_name)
# Define substitution strings so that the data is similar to BIDS
substitutions = [
('_subject_id_', 'sub-'), ('_resample_brain_flirt.nii_brain', ''),
('_roi_st_mcf_flirt.nii_brain_flirt', ''),
('task-rest_run-1_bold_roi_st_mcf.nii', 'motion_params'),
('T1w_resample_brain_flirt_sub-0050002_task-rest_run-1_bold_roi_st_mcf_mean_bet_flirt',
'fun2std')
]
# Feed the substitution strings to the DataSink node
dataSink.inputs.substitutions = substitutions
# ### Apply Mask to functional data
# Mean file of the motion corrected functional scan is sent to
# skullStrip to get just the brain and the mask_image.
# Mask_image is just a binary file (containing 1 where brain is present and 0 where it isn't).
# After getting the mask_image form skullStrip, apply that mask to aligned
# functional image to extract its brain and remove the skull
# In[889]:
# Function
# in_file: The file on which you want to apply mask
# in_file2 = mask_file: The mask you want to use. Make sure that mask_file has same size as in_file
# out_file : Result of applying mask in in_file -> Gives the path of the output file
def applyMask_func(in_file, in_file2):
import numpy as np
import nibabel as nib
import os
from os.path import join as opj
# convert from unicode to string : u'/tmp/tmp8daO2Q/..' -> '/tmp/tmp8daO2Q/..' i.e. removes the prefix 'u'
mask_file = in_file2
brain_data = nib.load(in_file)
mask_data = nib.load(mask_file)
brain = brain_data.get_data().astype('float32')
mask = mask_data.get_data()
# applying mask by multiplying elementwise to the binary mask
if len(brain.shape) == 3: # Anat file
brain = np.multiply(brain, mask)
elif len(brain.shape) > 3: # Functional File
for t in range(brain.shape[-1]):
brain[:, :, :, t] = np.multiply(brain[:, :, :, t], mask)
else:
pass
# Saving the brain file
path = os.getcwd()
in_file_split_list = in_file.split('/')
in_file_name = in_file_split_list[-1]
out_file = in_file_name + '_brain.nii.gz' # changing name
brain_with_header = nib.Nifti1Image(brain,
affine=brain_data.affine,
header=brain_data.header)
nib.save(brain_with_header, out_file)
out_file = opj(path, out_file)
out_file2 = in_file2
return out_file, out_file2
# #### Things learnt:
# 1. I found out that whenever a node is being executed, it becomes the current directory and whatever file you create now, will be stored here.
# 2. #from IPython.core.debugger import Tracer; Tracer()() # Debugger doesnt work in nipype
# Wrap the above function inside a Node
# In[890]:
applyMask = Node(Function(function=applyMask_func,
input_names=['in_file', 'in_file2'],
output_names=['out_file', 'out_file2']),
name='applyMask')
# ### Some nodes needed for Co-registration and Normalization
# Node for getting the xformation matrix
func2anat_reg = Node(FLIRT(output_type='NIFTI'), name="func2anat_reg")
# Node for applying xformation matrix to functional data
func2std_xform = Node(FLIRT(output_type='NIFTI', apply_xfm=True),
name="func2std_xform")
# Node for applying xformation matrix to functional data
std2func_xform = Node(FLIRT(output_type='NIFTI',
apply_xfm=True,
interp='nearestneighbour'),
name="std2func_xform")
# Node for Normalizing/Standardizing the anatomical and getting the xformation matrix
anat2std_reg = Node(FLIRT(output_type='NIFTI'), name="anat2std_reg")
# I wanted to use the MNI file as input to the workflow so I created an Identity
# Node that reads the MNI file path and outputs the same MNI file path.
# Then I connected this node to whereever it was needed.
MNI152_2mm = Node(IdentityInterface(fields=['standard_file', 'mask_file']),
name="MNI152_2mm")
# Set the mask_file and standard_file input in the Node. This setting sets the input mask_file permanently.
MNI152_2mm.inputs.mask_file = os.path.expandvars(
'$FSLDIR/data/standard/MNI152_T1_2mm_brain_mask.nii.gz')
MNI152_2mm.inputs.standard_file = os.path.expandvars(
'$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz')
# MNI152_2mm.inputs.mask_file = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain_mask.nii.gz'
# MNI152_2mm.inputs.standard_file = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
# ## Band Pass Filtering
# Let's do a band pass filtering on the data using the code from https://neurostars.org/t/bandpass-filtering-different-outputs-from-fsl-and-nipype-custom-function/824/2
### AFNI
bandpass = Node(afni.Bandpass(highpass=0.008,
lowpass=0.08,
despike=False,
no_detrend=True,
notrans=True,
outputtype='NIFTI_GZ'),
name='bandpass')
# ### Following is a Join Node that collects the preprocessed file paths and saves them in a file
# In[902]:
def save_file_list_function_in_brain(in_brain):
import numpy as np
import os
from os.path import join as opj
file_list = np.asarray(in_brain)
print('######################## File List ######################: \n',
file_list)
np.save('brain_file_list', file_list)
file_name = 'brain_file_list.npy'
out_brain = opj(os.getcwd(), file_name) # path
return out_brain
def save_file_list_function_in_mask(in_mask):
import numpy as np
import os
from os.path import join as opj
file_list2 = np.asarray(in_mask)
print('######################## File List ######################: \n',
file_list2)
np.save('mask_file_list', file_list2)
file_name2 = 'mask_file_list.npy'
out_mask = opj(os.getcwd(), file_name2) # path
return out_mask
def save_file_list_function_in_motion_params(in_motion_params):
import numpy as np
import os
from os.path import join as opj
file_list3 = np.asarray(in_motion_params)
print('######################## File List ######################: \n',
file_list3)
np.save('motion_params_file_list', file_list3)
file_name3 = 'motion_params_file_list.npy'
out_motion_params = opj(os.getcwd(), file_name3) # path
return out_motion_params
def save_file_list_function_in_motion_outliers(in_motion_outliers):
import numpy as np
import os
from os.path import join as opj
file_list4 = np.asarray(in_motion_outliers)
print('######################## File List ######################: \n',
file_list4)
np.save('motion_outliers_file_list', file_list4)
file_name4 = 'motion_outliers_file_list.npy'
out_motion_outliers = opj(os.getcwd(), file_name4) # path
return out_motion_outliers
def save_file_list_function_in_joint_xformation_matrix(
in_joint_xformation_matrix):
import numpy as np
import os
from os.path import join as opj
file_list5 = np.asarray(in_joint_xformation_matrix)
print('######################## File List ######################: \n',
file_list5)
np.save('joint_xformation_matrix_file_list', file_list5)
file_name5 = 'joint_xformation_matrix_file_list.npy'
out_joint_xformation_matrix = opj(os.getcwd(), file_name5) # path
return out_joint_xformation_matrix
def save_file_list_function_in_tr(in_tr):
import numpy as np
import os
from os.path import join as opj
tr_list = np.asarray(in_tr)
print('######################## TR List ######################: \n',
tr_list)
np.save('tr_list', tr_list)
file_name6 = 'tr_list.npy'
out_tr = opj(os.getcwd(), file_name6) # path
return out_tr
def save_file_list_function_in_atlas(in_atlas):
import numpy as np
import os
from os.path import join as opj
file_list7 = np.asarray(in_atlas)
print('######################## File List ######################: \n',
file_list7)
np.save('atlas_file_list', file_list7)
file_name7 = 'atlas_file_list.npy'
out_atlas = opj(os.getcwd(), file_name7) # path
return out_atlas
save_file_list_in_brain = JoinNode(Function(
function=save_file_list_function_in_brain,
input_names=['in_brain'],
output_names=['out_brain']),
joinsource="infosource",
joinfield=['in_brain'],
name="save_file_list_in_brain")
save_file_list_in_mask = JoinNode(Function(
function=save_file_list_function_in_mask,
input_names=['in_mask'],
output_names=['out_mask']),
joinsource="infosource",
joinfield=['in_mask'],
name="save_file_list_in_mask")
save_file_list_in_motion_outliers = JoinNode(
Function(function=save_file_list_function_in_motion_outliers,
input_names=['in_motion_outliers'],
output_names=['out_motion_outliers']),
joinsource="infosource",
joinfield=['in_motion_outliers'],
name="save_file_list_in_motion_outliers")
save_file_list_in_motion_params = JoinNode(
Function(function=save_file_list_function_in_motion_params,
input_names=['in_motion_params'],
output_names=['out_motion_params']),
joinsource="infosource",
joinfield=['in_motion_params'],
name="save_file_list_in_motion_params")
save_file_list_in_joint_xformation_matrix = JoinNode(
Function(function=save_file_list_function_in_joint_xformation_matrix,
input_names=['in_joint_xformation_matrix'],
output_names=['out_joint_xformation_matrix']),
joinsource="infosource",
joinfield=['in_joint_xformation_matrix'],
name="save_file_list_in_joint_xformation_matrix")
save_file_list_in_tr = JoinNode(Function(
function=save_file_list_function_in_tr,
input_names=['in_tr'],
output_names=['out_tr']),
joinsource="infosource",
joinfield=['in_tr'],
name="save_file_list_in_tr")
save_file_list_in_atlas = JoinNode(Function(
function=save_file_list_function_in_atlas,
input_names=['in_atlas'],
output_names=['out_atlas']),
joinsource="infosource",
joinfield=['in_atlas'],
name="save_file_list_in_atlas")
# save_file_list = JoinNode(Function(function=save_file_list_function, input_names=['in_brain', 'in_mask', 'in_motion_params','in_motion_outliers','in_joint_xformation_matrix', 'in_tr', 'in_atlas'],
# output_names=['out_brain','out_mask','out_motion_params','out_motion_outliers','out_joint_xformation_matrix','out_tr', 'out_atlas']),
# joinsource="infosource",
# joinfield=['in_brain', 'in_mask', 'in_motion_params','in_motion_outliers','in_joint_xformation_matrix','in_tr', 'in_atlas'],
# name="save_file_list")
# def save_file_list_function(in_brain, in_mask, in_motion_params, in_motion_outliers, in_joint_xformation_matrix, in_tr, in_atlas):
# # Imports
# import numpy as np
# import os
# from os.path import join as opj
#
#
# file_list = np.asarray(in_brain)
# print('######################## File List ######################: \n',file_list)
#
# np.save('brain_file_list',file_list)
# file_name = 'brain_file_list.npy'
# out_brain = opj(os.getcwd(),file_name) # path
#
#
# file_list2 = np.asarray(in_mask)
# print('######################## File List ######################: \n',file_list2)
#
# np.save('mask_file_list',file_list2)
# file_name2 = 'mask_file_list.npy'
# out_mask = opj(os.getcwd(),file_name2) # path
#
#
# file_list3 = np.asarray(in_motion_params)
# print('######################## File List ######################: \n',file_list3)
#
# np.save('motion_params_file_list',file_list3)
# file_name3 = 'motion_params_file_list.npy'
# out_motion_params = opj(os.getcwd(),file_name3) # path
#
#
# file_list4 = np.asarray(in_motion_outliers)
# print('######################## File List ######################: \n',file_list4)
#
# np.save('motion_outliers_file_list',file_list4)
# file_name4 = 'motion_outliers_file_list.npy'
# out_motion_outliers = opj(os.getcwd(),file_name4) # path
#
#
# file_list5 = np.asarray(in_joint_xformation_matrix)
# print('######################## File List ######################: \n',file_list5)
#
# np.save('joint_xformation_matrix_file_list',file_list5)
# file_name5 = 'joint_xformation_matrix_file_list.npy'
# out_joint_xformation_matrix = opj(os.getcwd(),file_name5) # path
#
# tr_list = np.asarray(in_tr)
# print('######################## TR List ######################: \n',tr_list)
#
# np.save('tr_list',tr_list)
# file_name6 = 'tr_list.npy'
# out_tr = opj(os.getcwd(),file_name6) # path
#
#
# file_list7 = np.asarray(in_atlas)
# print('######################## File List ######################: \n',file_list7)
#
# np.save('atlas_file_list',file_list7)
# file_name7 = 'atlas_file_list.npy'
# out_atlas = opj(os.getcwd(),file_name7) # path
#
#
#
#
# return out_brain, out_mask, out_motion_params, out_motion_outliers, out_joint_xformation_matrix, out_tr , out_atlas
#
#
#
# save_file_list = JoinNode(Function(function=save_file_list_function, input_names=['in_brain', 'in_mask', 'in_motion_params','in_motion_outliers','in_joint_xformation_matrix', 'in_tr', 'in_atlas'],
# output_names=['out_brain','out_mask','out_motion_params','out_motion_outliers','out_joint_xformation_matrix','out_tr', 'out_atlas']),
# joinsource="infosource",
# joinfield=['in_brain', 'in_mask', 'in_motion_params','in_motion_outliers','in_joint_xformation_matrix','in_tr', 'in_atlas'],
# name="save_file_list")
# ### Motion outliers
motionOutliers = Node(MotionOutliers(no_motion_correction=False,
metric='fd',
out_metric_plot='fd_plot.png',
out_metric_values='fd_raw.txt'),
name='motionOutliers')
# ## Workflow for atlas registration from std to functional
wf_atlas_resize_reg = Workflow(name=atlas_resize_reg_directory)
wf_atlas_resize_reg.connect([
# Apply the inverse matrix to the 3mm Atlas to transform it to func space
(maskfunc4mean, std2func_xform, [(('out_file', 'reference'))]),
(resample_atlas, std2func_xform, [('out_file', 'in_file')]),
# Now, applying the inverse matrix
(inv_mat, std2func_xform, [('out_file', 'in_matrix_file')]
), # output: Atlas in func space
(std2func_xform, save_file_list_in_atlas, [('out_file', 'in_atlas')]),
# ---------------------------Save the required files --------------------------------------------
(save_file_list_in_motion_params, dataSink,
[('out_motion_params', 'motion_params_paths.@out_motion_params')]),
(save_file_list_in_motion_outliers, dataSink,
[('out_motion_outliers', 'motion_outliers_paths.@out_motion_outliers')
]),
(save_file_list_in_brain, dataSink,
[('out_brain', 'preprocessed_brain_paths.@out_brain')]),
(save_file_list_in_mask, dataSink,
[('out_mask', 'preprocessed_mask_paths.@out_mask')]),
(save_file_list_in_joint_xformation_matrix, dataSink,
[('out_joint_xformation_matrix',
'joint_xformation_matrix_paths.@out_joint_xformation_matrix')]),
(save_file_list_in_tr, dataSink, [('out_tr', 'tr_paths.@out_tr')]),
(save_file_list_in_atlas, dataSink, [('out_atlas',
'atlas_paths.@out_atlas')])
])
# In[909]:
wf_coreg_reg = Workflow(name=coreg_reg_directory)
# wf_coreg_reg.base_dir = base_directory
# Dir where all the outputs will be stored(inside coregistrationPipeline folder).
if ANAT == 1:
wf_coreg_reg.connect(BIDSDataGrabber, 'anat_file_path', skullStrip,
'in_file') # Resampled the anat file to 3mm
wf_coreg_reg.connect(skullStrip, 'out_file', resample_anat, 'in_file')
wf_coreg_reg.connect(
resample_anat, 'out_file', func2anat_reg, 'reference'
) # Make the resampled file as reference in func2anat_reg
# Sec 1. The above 3 steps registers the mean image to resampled anat image and
# calculates the xformation matrix .. I hope the xformation matrix will be saved
wf_coreg_reg.connect(MNI152_2mm, 'standard_file', resample_mni,
'in_file')
wf_coreg_reg.connect(resample_mni, 'out_file', anat2std_reg,
'reference')
wf_coreg_reg.connect(resample_anat, 'out_file', anat2std_reg,
'in_file')
# Calculates the Xformationmatrix from anat3mm to MNI 3mm
# We can get those matrices by refering to func2anat_reg.outputs.out_matrix_file and similarly for anat2std_reg
wf_coreg_reg.connect(func2anat_reg, 'out_matrix_file', concat_xform,
'in_file')
wf_coreg_reg.connect(anat2std_reg, 'out_matrix_file', concat_xform,
'in_file2')
wf_coreg_reg.connect(concat_xform, 'out_file', dataSink,
'tranformation_matrix_fun2std.@out_file')
wf_coreg_reg.connect(concat_xform, 'out_file',
save_file_list_in_joint_xformation_matrix,
'in_joint_xformation_matrix')
# Now inverse the func2std MAT to std2func
wf_coreg_reg.connect(concat_xform, 'out_file', wf_atlas_resize_reg,
'inv_mat.in_file')
# ------------------------------------------------------------------------------------------------------------------------------
# Registration of Functional to MNI 3mm space w/o using anatomical
if ANAT == 0:
print('Not using Anatomical high resoulution files')
wf_coreg_reg.connect(MNI152_2mm, 'standard_file', resample_mni,
'in_file')
wf_coreg_reg.connect(
resample_mni, 'out_file', func2anat_reg, 'reference'
) # Make the resampled file as reference in func2anat_reg
wf_coreg_reg.connect(func2anat_reg, 'out_matrix_file', dataSink,
'tranformation_matrix_fun2std.@out_file')
wf_coreg_reg.connect(func2anat_reg, 'out_matrix_file',
save_file_list_in_joint_xformation_matrix,
'in_joint_xformation_matrix')
# Now inverse the func2std MAT to std2func
wf_coreg_reg.connect(func2anat_reg, 'out_matrix_file',
wf_atlas_resize_reg, 'inv_mat.in_file')
# ## Co-Registration, Normalization and Bandpass Workflow
# 1. Co-registration means alligning the func to anat
# 2. Normalization means aligning func/anat to standard
# 3. Applied band pass filtering in range - highpass=0.008, lowpass=0.08
# In[910]:
wf_motion_correction_bet = Workflow(name=motion_correction_bet_directory)
# wf_motion_correction_bet.base_dir = base_directory
wf_motion_correction_bet.connect([
(from_mcflirt, meanfunc, [('in_file', 'in_file')]),
(meanfunc, meanfuncmask, [('out_file', 'in_file')]),
(from_mcflirt, applyMask, [('in_file', 'in_file')]), # 1
(meanfuncmask, applyMask, [
('mask_file', 'in_file2')
]), # 2 output: 1&2, BET on coregistered fmri scan
(meanfunc, maskfunc4mean, [('out_file', 'in_file')]), # 3
(meanfuncmask, maskfunc4mean,
[('mask_file', 'in_file2')]), # 4 output: 3&4, BET on mean func scan
(applyMask, save_file_list_in_brain, [('out_file', 'in_brain')]),
(applyMask, save_file_list_in_mask, [('out_file2', 'in_mask')]),
(maskfunc4mean, wf_coreg_reg, [('out_file', 'func2anat_reg.in_file')])
])
infosource = Node(IdentityInterface(fields=['subject_id']),
name="infosource")
infosource.iterables = [('subject_id', subject_list)]
# Create the workflow
wf = Workflow(name=parent_wf_directory)
# base_dir = opj(s,'result')
wf.base_dir = base_directory # Dir where all the outputs will be stored(inside BETFlow folder).
# wf.connect([ (infosource, BIDSDataGrabber, [('subject_id','subject_id')]),
# (BIDSDataGrabber, extract, [('func_file_path','in_file')]),
#
# (BIDSDataGrabber,getMetadata, [('func_file_path','in_file')]),
#
# (getMetadata,slicetimer, [('tr','time_repetition')]),
#
#
# (getMetadata,slicetimer, [('index_dir','index_dir')]),
#
# (getMetadata,slicetimer, [('interleaved','interleaved')]),
#
# (getMetadata,save_file_list_in_tr, [('tr','in_tr')]),
#
# (extract,slicetimer,[('roi_file','in_file')]),
#
# (slicetimer, mcflirt,[('slice_time_corrected_file','in_file')])
# (mcflirt,dataSink,[('par_file','motion_params.@par_file')]), # saves the motion parameters calculated before
#
# (mcflirt,save_file_list_in_motion_params,[('par_file','in_motion_params')]),
#
# (mcflirt,wf_motion_correction_bet,[('out_file','from_mcflirt.in_file')])
# ])
# # Run it in parallel
# wf.run('MultiProc', plugin_args={'n_procs': num_proc})
#
#
#
# # Visualize the detailed graph
# # from IPython.display import Image
# wf.write_graph(graph2use='flat', format='png', simple_form=True)
# Options:
# discard 4 Volumes (extract), slicetimer, mcflirt
print('Preprocessing Options:')
print('Skipping 4 dummy volumes - ', options_binary_string[0])
print('Slicetiming correction - ', options_binary_string[1])
print('Finding Motion Outliers - ', options_binary_string[2])
print('Doing Motion Correction - ', options_binary_string[3])
# ANAT = 0
nodes = [extract, slicetimer, motionOutliers, mcflirt]
wf.connect(infosource, 'subject_id', BIDSDataGrabber, 'subject_id')
wf.connect(BIDSDataGrabber, 'func_file_path', getMetadata, 'in_file')
wf.connect(getMetadata, 'tr', save_file_list_in_tr, 'in_tr')
old_node = BIDSDataGrabber
old_node_output = 'func_file_path'
for idx, include in enumerate(options_binary_string):
if old_node == extract:
old_node_output = 'roi_file'
elif old_node == slicetimer:
old_node_output = 'slice_time_corrected_file'
# elif old_node == mcflirt:
# old_node_output = 'out_file'
if int(include):
new_node = nodes[idx]
if new_node == slicetimer:
wf.connect(getMetadata, 'tr', slicetimer, 'time_repetition')
wf.connect(getMetadata, 'index_dir', slicetimer, 'index_dir')
wf.connect(getMetadata, 'interleaved', slicetimer,
'interleaved')
new_node_input = 'in_file'
elif new_node == extract:
new_node_input = 'in_file'
elif new_node == mcflirt:
new_node_input = 'in_file'
wf.connect(mcflirt, 'par_file', dataSink,
'motion_params.@par_file'
) # saves the motion parameters calculated before
wf.connect(mcflirt, 'par_file',
save_file_list_in_motion_params, 'in_motion_params')
wf.connect(mcflirt, 'out_file', wf_motion_correction_bet,
'from_mcflirt.in_file')
elif new_node == motionOutliers:
wf.connect(meanfuncmask, 'mask_file', motionOutliers, 'mask')
wf.connect(motionOutliers, 'out_file', dataSink,
'motionOutliers.@out_file')
wf.connect(motionOutliers, 'out_metric_plot', dataSink,
'motionOutliers.@out_metric_plot')
wf.connect(motionOutliers, 'out_metric_values', dataSink,
'motionOutliers.@out_metric_values')
wf.connect(motionOutliers, 'out_file',
save_file_list_in_motion_outliers,
'in_motion_outliers')
new_node_input = 'in_file'
wf.connect(old_node, old_node_output, new_node, new_node_input)
continue
wf.connect(old_node, old_node_output, new_node, new_node_input)
old_node = new_node
else:
if idx == 3:
# new_node = from_mcflirt
# new_node_input = 'from_mcflirt.in_file'
wf.connect(old_node, old_node_output, wf_motion_correction_bet,
'from_mcflirt.in_file')
# old_node = new_node
TEMP_DIR_FOR_STORAGE = opj(base_directory, 'crash_files')
wf.config = {"execution": {"crashdump_dir": TEMP_DIR_FOR_STORAGE}}
# Visualize the detailed graph
# from IPython.display import Image
wf.write_graph(graph2use='flat', format='png', simple_form=True)
# Run it in parallel
wf.run('MultiProc', plugin_args={'n_procs': num_proc})
def _main(subject_list,vols,subid_vol_dict, number_of_skipped_volumes,brain_path,\
mask_path,\
atlas_path,\
tr_path,\
motion_params_path,\
func2std_mat_path,\
MNI3mm_path,\
base_directory,\
fc_datasink_name,\
motion_param_regression,\
band_pass_filtering,\
global_signal_regression,\
smoothing,\
volcorrect,\
num_proc,\
functional_connectivity_directory ):
# ## Volume correction
# * I have already extracted 4 volumes.
# * Now extract 120 - 4 = 116 volumes from each subject
# * So define vols = 114
#
if number_of_skipped_volumes == None:
number_of_skipped_volumes = 4
vols = vols - number_of_skipped_volumes
def vol_correct(sub_id, subid_vol_dict, vols, number_of_skipped_volumes):
sub_vols = subid_vol_dict[sub_id] - number_of_skipped_volumes
if sub_vols > vols:
t_min = sub_vols - vols
elif sub_vols == vols:
t_min = 0
else:
raise Exception('Volumes of Sub ',sub_id,' less than desired!')
return int(t_min)
# In[491]:
volCorrect = Node(Function(function=vol_correct, input_names=['sub_id','subid_vol_dict','vols','number_of_skipped_volumes'],
output_names=['t_min']), name='volCorrect')
volCorrect.inputs.subid_vol_dict = subid_vol_dict
volCorrect.inputs.vols = vols
volCorrect.inputs.number_of_skipped_volumes = number_of_skipped_volumes
# ## Define a function to fetch the filenames of a particular subject ID
def get_subject_filenames(subject_id,brain_path,mask_path,atlas_path,tr_path,motion_params_path,func2std_mat_path,MNI3mm_path):
import re
from itertools import zip_longest
for brain,mask,atlas,tr,motion_param,func2std_mat in zip_longest(brain_path,mask_path,atlas_path,tr_path,motion_params_path,func2std_mat_path): #itertools helps to zip unequal save_file_list_in_mask
# Source : https://stackoverflow.com/questions/11318977/zipping-unequal-lists-in-python-in-to-a-list-which-does-not-drop-any-element-fro
print('*******************',brain,mask,atlas,tr,motion_param,func2std_mat)
sub_id_extracted = re.search('.+_subject_id_(\d+)', brain).group(1)
if str(subject_id) in brain:
# print("Files for subject ",subject_id,brain,mask,atlas,tr,motion_param)
return brain,mask,atlas,tr,motion_param,func2std_mat,MNI3mm_path
print ('Unable to locate Subject: ',subject_id,'extracted: ',sub_id_extracted)
# print ('Unable to locate Subject: ',subject_id)
raise Exception('Unable to locate Subject: ',subject_id,'extracted: ',sub_id_extracted)
# raise Exception('Unable to locate Subject: ',subject_id)
return 0
# Make a node
getSubjectFilenames = Node(Function(function=get_subject_filenames, input_names=['subject_id','brain_path','mask_path','atlas_path','tr_path','motion_params_path','func2std_mat_path','MNI3mm_path'],
output_names=['brain','mask','atlas','tr','motion_param','func2std_mat', 'MNI3mm_path']), name='getSubjectFilenames')
getSubjectFilenames.inputs.brain_path = brain_path
getSubjectFilenames.inputs.mask_path = mask_path
getSubjectFilenames.inputs.atlas_path = atlas_path
getSubjectFilenames.inputs.tr_path = tr_path
getSubjectFilenames.inputs.motion_params_path = motion_params_path
getSubjectFilenames.inputs.func2std_mat_path = func2std_mat_path
getSubjectFilenames.inputs.MNI3mm_path = MNI3mm_path
infosource = Node(IdentityInterface(fields=['subject_id']),
name="infosource")
infosource.iterables = [('subject_id',subject_list)]
# ## Band Pass Filtering
# Let's do a band pass filtering on the data using the
# code from https://neurostars.org/t/bandpass-filtering-different-outputs-from-fsl-and-nipype-custom-function/824/2
### AFNI
bandpass = Node(afni.Bandpass(highpass=0.01, lowpass=0.1,
despike=False, no_detrend=True, notrans=True,
outputtype='NIFTI_GZ'),name='bandpass')
# bandpass = Node(afni.Bandpass(highpass=0.001, lowpass=0.01,
# despike=False, no_detrend=True, notrans=True,
# tr=2.0,outputtype='NIFTI_GZ'),name='bandpass')
# ## Highpass filtering
# In[506]:
"""
Perform temporal highpass filtering on the data
"""
# https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBandpass.html
# os.chdir('/home1/varunk/Autism-Connectome-Analysis-bids-related/')
highpass = Node(afni.Bandpass(highpass=0.009, lowpass=99999,
despike=False, no_detrend=True, notrans=True,
outputtype='NIFTI_GZ'),name='highpass')
# FSL bandpass/Highpass
# highpass = Node(interface=ImageMaths(suffix='_tempfilt'),
# iterfield=['in_file'],
# name='highpass')
#
# highpass.inputs.op_string = '-bptf 27.77775001525879 -1' # 23.64 # 31.25
# ## Smoothing
# ### Using 6mm fwhm
# sigma = 6/2.3548 = 2.547987090198743
spatialSmooth = Node(interface=ImageMaths(op_string='-s 2.5479',
suffix='_smoothed'),
name='spatialSmooth')
# ## Performs Gram Schmidt Process
# https://en.wikipedia.org/wiki/Gram%E2%80%93Schmidt_process
# In[509]:
def orthogonalize(in_file, mask_file):
import numpy as np
import nibabel as nib
import os
from os.path import join as opj
def gram_schmidt(voxel_time_series, mean_vector):
numerator = np.dot(voxel_time_series,mean_vector)
dinominator = np.dot(mean_vector,mean_vector)
voxel_time_series_orthogonalized = voxel_time_series - (numerator/dinominator)*mean_vector
# TO CONFIRM IF THE VECTORS ARE ORTHOGONAL
# sum_dot_prod = np.sum(np.dot(voxel_time_series_orthogonalized,mean_vector))
# print('Sum of entries of orthogonalized vector = ',sum_dot_prod)
return voxel_time_series_orthogonalized
mask_data = nib.load(mask_file)
mask = mask_data.get_data()
brain_data = nib.load(in_file)
brain = brain_data.get_data()
x_dim, y_dim, z_dim, t_dim = brain_data.shape
# Find mean brain
mean_vector = np.zeros(t_dim)
num_brain_voxels = 0
# Count the number of brain voxels
for i in range(x_dim):
for j in range(y_dim):
for k in range(z_dim):
if mask[i,j,k] == 1:
mean_vector = mean_vector + brain[i,j,k,:]
num_brain_voxels = num_brain_voxels + 1
mean_vector = mean_vector / num_brain_voxels
# Orthogonalize
for i in range(x_dim):
for j in range(y_dim):
for k in range(z_dim):
if mask[i,j,k] == 1:
brain[i,j,k,:] = gram_schmidt(brain[i,j,k,:], mean_vector)
sub_id = in_file.split('/')[-1].split('.')[0].split('_')[0].split('-')[1]
gsr_file_name = 'sub-' + sub_id + '_task-rest_run-1_bold.nii.gz'
# gsr_file_name_nii = gsr_file_name + '.nii.gz'
out_file = opj(os.getcwd(),gsr_file_name) # path
brain_with_header = nib.Nifti1Image(brain, affine=brain_data.affine,header = brain_data.header)
nib.save(brain_with_header,gsr_file_name)
return out_file
# In[510]:
globalSignalRemoval = Node(Function(function=orthogonalize, input_names=['in_file','mask_file'],
output_names=['out_file']), name='globalSignalRemoval' )
# globalSignalRemoval.inputs.mask_file = mask_file
# globalSignalRemoval.iterables = [('in_file',file_paths)]
# ## GLM for regression of motion parameters
# In[511]:
def calc_residuals(in_file,
motion_file):
"""
Calculates residuals of nuisance regressors -motion parameters for every voxel for a subject using GLM.
Parameters
----------
in_file : string
Path of a subject's motion corrected nifti file.
motion_par_file : string
path of a subject's motion parameters
Returns
-------
out_file : string
Path of residual file in nifti format
"""
import nibabel as nb
import numpy as np
import os
from os.path import join as opj
nii = nb.load(in_file)
data = nii.get_data().astype(np.float32)
global_mask = (data != 0).sum(-1) != 0
# Check and define regressors which are provided from files
if motion_file is not None:
motion = np.genfromtxt(motion_file)
if motion.shape[0] != data.shape[3]:
raise ValueError('Motion parameters {0} do not match data '
'timepoints {1}'.format(motion.shape[0],
data.shape[3]))
if motion.size == 0:
raise ValueError('Motion signal file {0} is '
'empty'.format(motion_file))
# Calculate regressors
regressor_map = {'constant' : np.ones((data.shape[3],1))}
regressor_map['motion'] = motion
X = np.zeros((data.shape[3], 1))
for rname, rval in regressor_map.items():
X = np.hstack((X, rval.reshape(rval.shape[0],-1)))
X = X[:,1:]
if np.isnan(X).any() or np.isnan(X).any():
raise ValueError('Regressor file contains NaN')
Y = data[global_mask].T
try:
B = np.linalg.inv(X.T.dot(X)).dot(X.T).dot(Y)
except np.linalg.LinAlgError as e:
if "Singular matrix" in e:
raise Exception("Error details: {0}\n\nSingular matrix error: "
"The nuisance regression configuration you "
"selected may have been too stringent, and the "
"regression could not be completed. Ensure your "
"parameters are not too "
"extreme.\n\n".format(e))
else:
raise Exception("Error details: {0}\n\nSomething went wrong with "
"nuisance regression.\n\n".format(e))
Y_res = Y - X.dot(B)
data[global_mask] = Y_res.T
img = nb.Nifti1Image(data, header=nii.get_header(),
affine=nii.get_affine())
subject_name = in_file.split('/')[-1].split('.')[0]
filename = subject_name + '_residual.nii.gz'
out_file = os.path.join(os.getcwd(),filename )
img.to_filename(out_file) # alt to nib.save
return out_file
# In[512]:
# Create a Node for above
calc_residuals = Node(Function(function=calc_residuals, input_names=['in_file','motion_file'],
output_names=['out_file']), name='calc_residuals')
# ## Datasink
# I needed to define the structure of what files are saved and where.
# In[513]:
# Create DataSink object
dataSink = Node(DataSink(), name='datasink')
# Name of the output folder
dataSink.inputs.base_directory = opj(base_directory,fc_datasink_name)
# To create the substitutions I looked the `datasink` folder where I was redirecting the output. I manually selected the part of file/folder name that I wanted to change and copied below to be substituted.
#
# In[514]:
# Define substitution strings so that the data is similar to BIDS
substitutions = [('_subject_id_', 'sub-')]
# Feed the substitution strings to the DataSink node
dataSink.inputs.substitutions = substitutions
# ### Following is a Join Node that collects the preprocessed file paths and saves them in a file
# In[516]:
def save_file_list_function(in_fc_map_brain_file):
# Imports
import numpy as np
import os
from os.path import join as opj
file_list = np.asarray(in_fc_map_brain_file)
print('######################## File List ######################: \n',file_list)
np.save('fc_map_brain_file_list',file_list)
file_name = 'fc_map_brain_file_list.npy'
out_fc_map_brain_file = opj(os.getcwd(),file_name) # path
return out_fc_map_brain_file
# In[517]:
save_file_list = JoinNode(Function(function=save_file_list_function, input_names=['in_fc_map_brain_file'],
output_names=['out_fc_map_brain_file']),
joinsource="infosource",
joinfield=['in_fc_map_brain_file'],
name="save_file_list")
# ## Create a FC node
#
# This node:
# 1. Exracts the average time series of the brain ROI's using the atlas and stores
# it as a matrix of size [ROIs x Volumes].
# 2. Extracts the Voxel time series and stores it in matrix of size [Voxels x Volumes]
#
# And save FC matrix files in shape of brains
def pear_coff(in_file, atlas_file, mask_file):
# code to find how many voxels are in the brain region using the mask
# imports
import numpy as np
import nibabel as nib
import os
from os.path import join as opj
mask_data = nib.load(mask_file)
mask = mask_data.get_data()
x_dim, y_dim, z_dim = mask_data.shape
atlasPath = atlas_file
# Read the atlas
atlasObject = nib.load(atlasPath)
atlas = atlasObject.get_data()
num_ROIs = int((np.max(atlas) - np.min(atlas) ))
# Read the brain in_file
brain_data = nib.load(in_file)
brain = brain_data.get_data()
x_dim, y_dim, z_dim, num_volumes = brain.shape
num_brain_voxels = 0
x_dim, y_dim, z_dim = mask_data.shape
for i in range(x_dim):
for j in range(y_dim):
for k in range(z_dim):
if mask[i,j,k] == 1:
num_brain_voxels = num_brain_voxels + 1
# Initialize a matrix of ROI time series and voxel time series
ROI_matrix = np.zeros((num_ROIs, num_volumes))
voxel_matrix = np.zeros((num_brain_voxels, num_volumes))
# Fill up the voxel_matrix
voxel_counter = 0
for i in range(x_dim):
for j in range(y_dim):
for k in range(z_dim):
if mask[i,j,k] == 1:
voxel_matrix[voxel_counter,:] = brain[i,j,k,:]
voxel_counter = voxel_counter + 1
# Fill up the ROI_matrix
# Keep track of number of voxels per ROI as well by using an array - num_voxels_in_ROI[]
num_voxels_in_ROI = np.zeros((num_ROIs,1)) # A column arrray containing number of voxels in each ROI
for i in range(x_dim):
for j in range(y_dim):
for k in range(z_dim):
label = int(atlas[i,j,k]) - 1
if label != -1:
ROI_matrix[label,:] = np.add(ROI_matrix[label,:], brain[i,j,k,:])
num_voxels_in_ROI[label,0] = num_voxels_in_ROI[label,0] + 1
ROI_matrix = np.divide(ROI_matrix,num_voxels_in_ROI) # Check if divide is working correctly
X, Y = ROI_matrix, voxel_matrix
# Subtract mean from X and Y
X = np.subtract(X, np.mean(X, axis=1, keepdims=True))
Y = np.subtract(Y, np.mean(Y, axis=1, keepdims=True))
temp1 = np.dot(X,Y.T)
temp2 = np.sqrt(np.sum(np.multiply(X,X), axis=1, keepdims=True))
temp3 = np.sqrt(np.sum(np.multiply(Y,Y), axis=1, keepdims=True))
temp4 = np.dot(temp2,temp3.T)
coff_matrix = np.divide(temp1, (temp4 + 1e-7))
# Check if any ROI is missing and replace the NAN values in coff_matrix by 0
if np.argwhere(np.isnan(coff_matrix)).shape[0] != 0:
print("Some ROIs are not present. Replacing NAN in coff matrix by 0")
np.nan_to_num(coff_matrix, copy=False)
# TODO: when I have added 1e-7 in the dinominator, then why did I feel the need to replace NAN by zeros
sub_id = in_file.split('/')[-1].split('.')[0].split('_')[0].split('-')[1]
fc_file_name = sub_id + '_fc_map'
print ("Pear Matrix calculated for subject: ",sub_id)
roi_brain_matrix = coff_matrix
brain_file = in_file
x_dim, y_dim, z_dim, t_dim = brain.shape
(brain_data.header).set_data_shape([x_dim,y_dim,z_dim,num_ROIs])
brain_roi_tensor = np.zeros((brain_data.header.get_data_shape()))
print("Creating brain for Subject-",sub_id)
for roi in range(num_ROIs):
brain_voxel_counter = 0
for i in range(x_dim):
for j in range(y_dim):
for k in range(z_dim):
if mask[i,j,k] == 1:
brain_roi_tensor[i,j,k,roi] = roi_brain_matrix[roi,brain_voxel_counter]
brain_voxel_counter = brain_voxel_counter + 1
assert (brain_voxel_counter == len(roi_brain_matrix[roi,:]))
print("Created brain for Subject-",sub_id)
path = os.getcwd()
fc_file_name = fc_file_name + '.nii.gz'
out_file = opj(path,fc_file_name)
brain_with_header = nib.Nifti1Image(brain_roi_tensor, affine=brain_data.affine,header = brain_data.header)
nib.save(brain_with_header,out_file)
fc_map_brain_file = out_file
return fc_map_brain_file
# In[521]:
# Again Create the Node and set default values to paths
pearcoff = Node(Function(function=pear_coff, input_names=['in_file','atlas_file','mask_file'],
output_names=['fc_map_brain_file']), name='pearcoff')
# # IMPORTANT:
# * The ROI 255 has been removed due to resampling. Therefore the FC maps will have nan at that row. So don't use that ROI :)
# * I came to know coz I keep getting this error: RuntimeWarning: invalid value encountered in true_divide
# * To debug it, I read the coff matrix and checked its diagnol to discover the nan value.
#
#
#
# ## Extract volumes
# ExtractROI - For volCorrect
extract = Node(ExtractROI(t_size=-1),
output_type='NIFTI',
name="extract")
# ### Node for applying xformation matrix to functional data
#
# In[523]:
func2std_xform = Node(FLIRT(output_type='NIFTI_GZ',
apply_xfm=True), name="func2std_xform")
# motion_param_regression = 1
# band_pass_filtering = 0
# global_signal_regression = 0
# smoothing = 1
# volcorrect = 1
if num_proc == None:
num_proc = 7
combination = 'motionRegress' + str(int(motion_param_regression)) + \
'global' + str(int(global_signal_regression)) + 'smoothing' + str(int(smoothing)) +\
'filt' + str(int(band_pass_filtering))
print("Combination: ",combination)
binary_string = str(int(motion_param_regression)) + str(int(global_signal_regression)) + \
str(int(smoothing)) + str(int(band_pass_filtering)) + str(int(volcorrect))
base_dir = opj(base_directory,functional_connectivity_directory)
# wf = Workflow(name=functional_connectivity_directory)
wf = Workflow(name=combination)
wf.base_dir = base_dir # Dir where all the outputs will be stored.
wf.connect(infosource ,'subject_id', getSubjectFilenames, 'subject_id')
# ------- Dynamic Pipeline ------------------------
nodes = [
calc_residuals,
globalSignalRemoval,
spatialSmooth,
bandpass,
volCorrect]
# from nipype.interfaces import fsl
old_node = getSubjectFilenames
old_node_output = 'brain'
binary_string = binary_string+'0' # so that the loop runs one more time
for idx, include in enumerate(binary_string):
# 11111
# motion_param_regression
# global_signal_regression
# smoothing
# band_pass_filtering
# volcorrect
if old_node == calc_residuals:
old_node_output = 'out_file'
elif old_node == extract :
old_node_output = 'roi_file'
elif old_node == globalSignalRemoval:
old_node_output = 'out_file'
elif old_node == bandpass:
old_node_output = 'out_file'
elif old_node == highpass:
old_node_output = 'out_file'
elif old_node == spatialSmooth:
old_node_output = 'out_file'
elif old_node == volCorrect:
old_node_output = 'out_file'
if int(include):
# if old_node is None:
#
# wf.add_nodes([nodes[idx]])
#
# else:
new_node = nodes[idx]
if new_node == calc_residuals:
wf.connect([(getSubjectFilenames, calc_residuals, [('motion_param', 'motion_file')])])
new_node_input = 'in_file'
elif new_node == extract :
wf.connect([( volCorrect, extract, [('t_min','t_min')])])
new_node_input = 'in_file'
elif new_node == globalSignalRemoval:
wf.connect([(getSubjectFilenames, globalSignalRemoval, [('mask','mask_file')])])
new_node_input = 'in_file'
elif new_node == bandpass:
wf.connect([(getSubjectFilenames, bandpass, [('tr','tr')])])
new_node_input = 'in_file'
elif new_node == highpass:
wf.connect([(getSubjectFilenames, highpass, [('tr','tr')])]) #Commenting for FSL
new_node_input = 'in_file'
elif new_node == spatialSmooth:
new_node_input = 'in_file'
elif new_node == volCorrect:
wf.connect([(infosource, volCorrect, [('subject_id','sub_id')])])
wf.connect([( volCorrect, extract, [('t_min','t_min')])])
new_node = extract
new_node_input = 'in_file'
wf.connect(old_node, old_node_output, new_node, new_node_input)
old_node = new_node
else:
if idx == 3: # bandpas == 0 => Highpass
new_node = highpass
wf.connect([(getSubjectFilenames, highpass, [('tr','tr')])]) #Commenting for FSL
new_node_input = 'in_file'
wf.connect(old_node, old_node_output, new_node, new_node_input)
old_node = new_node
wf.connect(old_node, old_node_output, pearcoff, 'in_file')
wf.connect(getSubjectFilenames,'atlas', pearcoff, 'atlas_file')
wf.connect(getSubjectFilenames, 'mask', pearcoff, 'mask_file')
wf.connect(pearcoff, 'fc_map_brain_file', func2std_xform ,'in_file')
wf.connect(getSubjectFilenames,'func2std_mat', func2std_xform, 'in_matrix_file')
wf.connect(getSubjectFilenames, 'MNI3mm_path', func2std_xform,'reference')
folder_name = combination + '.@fc_map_brain_file'
wf.connect(func2std_xform, 'out_file', save_file_list, 'in_fc_map_brain_file')
wf.connect(save_file_list, 'out_fc_map_brain_file', dataSink,folder_name)
TEMP_DIR_FOR_STORAGE = opj(base_directory,'crash_files')
wf.config = {"execution": {"crashdump_dir": TEMP_DIR_FOR_STORAGE}}
wf.write_graph(graph2use='flat', format='png')
wf.run('MultiProc', plugin_args={'n_procs': num_proc})
def canonical(
subjects_participants,
regdir,
f2s,
template="~/GitHub/mriPipeline/templates/waxholm/WHS_SD_rat_T2star_v1.01_downsample3.nii.gz",
f_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
):
"""Warp a functional image based on the functional-to-structural and the structural-to-template registrations.
Currently this approach is failing because the functiona-to-structural registration pushes the brain stem too far down.
This may be
"""
template = os.path.expanduser(template)
for subject_participant in subjects_participants:
func_image_dir = os.path.expanduser(
f_file_format.format(**subject_participant))
struct_image_dir = os.path.expanduser(
s_file_format.format(**subject_participant))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir, myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir, myfile)
except FileNotFoundError:
pass
else:
#struct
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}/ss_n4_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500, 500, 500, 500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}/ss__n4_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET_res = struct_BET.run()
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0, ),
(1.0, 3.0, 5.0)
] ##
struct_registration.inputs.number_of_iterations = [[
2000, 1000, 500
], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11,
1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1],
[4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [
True, True
]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = 6
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}/s_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
struct_registration_res = struct_registration.run()
#func
func_n4 = ants.N4BiasFieldCorrection()
func_n4.inputs.dimension = 3
func_n4.inputs.input_image = func_image
func_n4.inputs.bspline_fitting_distance = 100
func_n4.inputs.shrink_factor = 2
func_n4.inputs.n_iterations = [200, 200, 200, 200]
func_n4.inputs.convergence_threshold = 1e-11
func_n4.inputs.output_image = '{}/f_n4_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
func_n4_res = func_n4.run()
func_registration = ants.Registration()
func_registration.inputs.fixed_image = n4_res.outputs.output_image
func_registration.inputs.output_transform_prefix = "func_"
func_registration.inputs.transforms = [f2s]
func_registration.inputs.transform_parameters = [(0.1, )]
func_registration.inputs.number_of_iterations = [[40, 20, 10]]
func_registration.inputs.dimension = 3
func_registration.inputs.write_composite_transform = True
func_registration.inputs.collapse_output_transforms = True
func_registration.inputs.initial_moving_transform_com = True
func_registration.inputs.metric = ['MeanSquares']
func_registration.inputs.metric_weight = [1]
func_registration.inputs.radius_or_number_of_bins = [16]
func_registration.inputs.sampling_strategy = ["Regular"]
func_registration.inputs.sampling_percentage = [0.3]
func_registration.inputs.convergence_threshold = [1.e-2]
func_registration.inputs.convergence_window_size = [8]
func_registration.inputs.smoothing_sigmas = [[4, 2,
1]] # [1,0.5,0]
func_registration.inputs.sigma_units = ['vox']
func_registration.inputs.shrink_factors = [[3, 2, 1]]
func_registration.inputs.use_estimate_learning_rate_once = [True]
func_registration.inputs.use_histogram_matching = [False]
func_registration.inputs.winsorize_lower_quantile = 0.005
func_registration.inputs.winsorize_upper_quantile = 0.995
func_registration.inputs.args = '--float'
func_registration.inputs.num_threads = 6
func_registration.inputs.moving_image = func_n4_res.outputs.output_image
func_registration.inputs.output_warped_image = '{}/f_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
func_registration_res = func_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False, False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}/{}_ofM{}.nii.gz'.format(
regdir, participant, i)
warp.num_threads = 6
warp.inputs.input_image = func_image
warp.inputs.transforms = [
func_registration_res.outputs.composite_transform,
struct_registration_res.outputs.composite_transform
]
warp.run()
def functional_per_participant_test():
for i in ["", "_aF", "_cF1", "_cF2", "_pF"]:
template = "~/ni_data/templates/ds_QBI_chr.nii.gz"
participant = "4008"
image_dir = "~/ni_data/ofM.dr/preprocessing/generic_work/_subject_session_{}.ofM{}/_scan_type_7_EPI_CBV/temporal_mean/".format(
participant, i)
try:
for myfile in os.listdir(image_dir):
if myfile.endswith(".nii.gz"):
mimage = os.path.join(image_dir, myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = mimage
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = 'n4_{}_ofM{}.nii.gz'.format(
participant, i)
n4_res = n4.run()
functional_cutoff = ImageMaths()
functional_cutoff.inputs.op_string = "-thrP 30"
functional_cutoff.inputs.in_file = n4_res.outputs.output_image
functional_cutoff_res = functional_cutoff.run()
functional_BET = BET()
functional_BET.inputs.mask = True
functional_BET.inputs.frac = 0.5
functional_BET.inputs.in_file = functional_cutoff_res.outputs.out_file
functional_BET_res = functional_BET.run()
registration = ants.Registration()
registration.inputs.fixed_image = template
registration.inputs.output_transform_prefix = "output_"
registration.inputs.transforms = ['Affine', 'SyN']
registration.inputs.transform_parameters = [(0.1, ),
(3.0, 3.0, 5.0)]
registration.inputs.number_of_iterations = [[10000, 10000, 10000],
[100, 100, 100]]
registration.inputs.dimension = 3
registration.inputs.write_composite_transform = True
registration.inputs.collapse_output_transforms = True
registration.inputs.initial_moving_transform_com = True
registration.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
registration.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
registration.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
registration.inputs.sampling_strategy = ['Regular'] * 2 + [[
None, None
]]
registration.inputs.sampling_percentage = [0.3] * 2 + [[
None, None
]]
registration.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
registration.inputs.convergence_window_size = [20] * 2 + [5]
registration.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[
1, 0.5, 0
]]
registration.inputs.sigma_units = ['vox'] * 3
registration.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
registration.inputs.use_estimate_learning_rate_once = [True] * 3
registration.inputs.use_histogram_matching = [False] * 2 + [True]
registration.inputs.winsorize_lower_quantile = 0.005
registration.inputs.winsorize_upper_quantile = 0.995
registration.inputs.args = '--float'
registration.inputs.num_threads = 4
registration.plugin_args = {
'qsub_args': '-pe orte 4',
'sbatch_args': '--mem=6G -c 4'
}
registration.inputs.moving_image = functional_BET_res.outputs.out_file
registration.inputs.output_warped_image = '{}_ofM{}.nii.gz'.format(
participant, i)
res = registration.run()
def get_wf_tissue_priors(name='wf_tissue_priors3'):
'''
This Function gives a workflow that Resamples the tissue priors and then thresholds it at 0.5
'''
# csf_tissue_prior_path, gm_tissue_prior_path, wm_tissue_prior_path,
# threshold = 0.5
wf_tissue_priors = Workflow(name=name)
inputspec = Node(IdentityInterface(fields=['csf_tissue_prior_path', 'wm_tissue_prior_path',
'threshold','std2func_mat_path', 'reference_func_file_path']),
name="inputspec")
'''
# 'gm_tissue_prior_path',
resample_tissue_prior_csf = Node(Resample(voxel_size=(3, 3, 3), resample_mode='Cu', # cubic interpolation
outputtype='NIFTI'),
name="resample_tissue_prior_csf")
# resample_tissue_prior_gm = Node(Resample(voxel_size=(3, 3, 3), resample_mode='Cu', # cubic interpolation
# outputtype='NIFTI'),
# name="resample_tissue_prior_gm")
resample_tissue_prior_wm = Node(Resample(voxel_size=(3, 3, 3), resample_mode='Cu', # cubic interpolation
outputtype='NIFTI'),
name="resample_tissue_prior_wm")
wf_tissue_priors.connect(inputspec, 'csf_tissue_prior_path', resample_tissue_prior_csf, 'in_file' )
# wf_tissue_priors.connect(inputspec, 'gm_tissue_prior_path', resample_tissue_prior_gm, 'in_file' )
wf_tissue_priors.connect(inputspec, 'wm_tissue_prior_path', resample_tissue_prior_wm, 'in_file' )
'''
# # Invert the func2anat matrix to get anat2func
# inv_mat = Node(ConvertXFM(invert_xfm=True), name='inv_mat')
# wf_tissue_priors.connect(inputspec, 'func2anat_mat_path', inv_mat, 'in_file')
# Transform the tissue priors to the functional space using the inverse matrix
std2func_xform_csf_prior = Node(FLIRT(output_type='NIFTI',
apply_xfm=True, interp='sinc'), name='std2func_xform_csf_prior')
wf_tissue_priors.connect(inputspec, 'reference_func_file_path', std2func_xform_csf_prior, 'reference')
wf_tissue_priors.connect(inputspec, 'std2func_mat_path', std2func_xform_csf_prior, 'in_matrix_file')
std2func_xform_wm_prior = Node(FLIRT(output_type='NIFTI',
apply_xfm=True, interp='sinc'), name='std2func_xform_wm_prior')
wf_tissue_priors.connect(inputspec, 'reference_func_file_path', std2func_xform_wm_prior, 'reference')
wf_tissue_priors.connect(inputspec, 'std2func_mat_path', std2func_xform_wm_prior, 'in_matrix_file')
# Transformed the priors
# Get the input in_file(s) of the std2func_xform_csf and std2func_xform_wm from the old workspace
wf_tissue_priors.connect(inputspec, 'csf_tissue_prior_path', std2func_xform_csf_prior, 'in_file')
wf_tissue_priors.connect(inputspec, 'wm_tissue_prior_path', std2func_xform_wm_prior, 'in_file')
# Threshold
def get_opstring(threshold, tissue_type):
if tissue_type == 'csf':
max = 216 # 216 is the highest intensity of the resampled afni output for CSF
elif tissue_type == 'wm':
max = 253 # 253 is the highest intensity of the resampled afni output for WM
threshold = int(threshold * max)
op = '-thr '+str(threshold)+' -bin'
return op
# ----- CSF ------
threshold_csf = Node(interface=ImageMaths(suffix='_thresh'),
name='threshold_csf')
wf_tissue_priors.connect(inputspec, ('threshold', get_opstring, 'csf'), threshold_csf, 'op_string' )
wf_tissue_priors.connect(std2func_xform_csf_prior, 'out_file', threshold_csf, 'in_file')
# ------- GM --------
# threshold_gm = Node(interface=ImageMaths(suffix='_thresh'),
# name='threshold_gm')
# wf_tissue_priors.connect(inputspec, ('threshold', get_opstring), threshold_gm, 'op_string' )
# wf_tissue_priors.connect(resample_tissue_prior_gm, 'out_file', threshold_gm, 'in_file')
# -------- WM --------
threshold_wm = Node(interface=ImageMaths(suffix='_thresh'),
name='threshold_wm')
wf_tissue_priors.connect(inputspec, ('threshold', get_opstring, 'wm'), threshold_wm, 'op_string' )
wf_tissue_priors.connect(std2func_xform_wm_prior, 'out_file', threshold_wm, 'in_file')
# -------------------
outputspec = Node(IdentityInterface(fields=['csf_tissue_prior_path', 'wm_tissue_prior_path', 'threshold']),
name="outputspec")
# , 'gm_tissue_prior_path'
wf_tissue_priors.connect(threshold_csf, 'out_file', outputspec, 'csf_tissue_prior_path')
# wf_tissue_priors.connect(threshold_gm, 'out_file', outputspec, 'gm_tissue_prior_path')
wf_tissue_priors.connect(threshold_wm, 'out_file', outputspec, 'wm_tissue_prior_path')
return wf_tissue_priors
def create_fatsegnet_workflow(
subject_list,
bids_dir,
work_dir,
out_dir,
bids_templates,
n4=False
):
# create initial workflow
wf = Workflow(name='workflow_fatsegnet', base_dir=work_dir)
# use infosource to iterate workflow across subject list
n_infosource = Node(
interface=IdentityInterface(
fields=['subject_id']
),
name="subject_source"
# input: 'subject_id'
# output: 'subject_id'
)
# runs the node with subject_id = each element in subject_list
n_infosource.iterables = ('subject_id', subject_list)
# select matching files from bids_dir
n_selectfiles = Node(
interface=SelectFiles(
templates=bids_templates,
base_directory=bids_dir
),
name='get_subject_data'
# output: ['fat_composed', 'water_composed']
)
wf.connect([
(n_infosource, n_selectfiles, [('subject_id', 'subject_id_p')])
])
if n4:
mn_n4_fat = Node(
interface=N4BiasFieldCorrection(),
iterfield=['input_image'],
name='N4_fat',
# output: 'output_image'
)
wf.connect([
(n_selectfiles, mn_n4_fat, [('fat_composed', 'input_image')]),
])
# https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.ants.html
mn_n4_water = Node(
interface=N4BiasFieldCorrection(),
iterfield=['input_image'],
name='N4_water',
# output: 'output_image'
)
wf.connect([
(n_selectfiles, mn_n4_water, [('water_composed', 'input_image')]),
])
# scale data
# or better: https://intensity-normalization.readthedocs.io/en/latest/utilities.html
def scale(min_and_max):
min_value = min_and_max[0][0]
max_value = min_and_max[0][1]
fsl_cmd = ""
# set range to [0, 2pi]
fsl_cmd += "-mul %.10f " % (4)
return fsl_cmd
mn_fat_stats = MapNode(
# -R : <min intensity> <max intensity>
interface=ImageStats(op_string='-R'),
iterfield=['in_file'],
name='get_stats_fat',
# output: 'out_stat'
)
mn_water_stats = MapNode(
# -R : <min intensity> <max intensity>
interface=ImageStats(op_string='-R'),
iterfield=['in_file'],
name='get_stats_water',
# output: 'out_stat'
)
if n4:
wf.connect([
(mn_n4_fat, mn_fat_stats, [('output_image', 'in_file')]),
(mn_n4_water, mn_water_stats, [('output_image', 'in_file')])
])
else:
wf.connect([
(n_selectfiles, mn_fat_stats, [('fat_composed', 'in_file')]),
(n_selectfiles, mn_water_stats, [('water_composed', 'in_file')])
])
mn_fat_scaled = Node(
interface=ImageMaths(suffix="_scaled"),
name='fat_scaled',
iterfield=['in_file']
# inputs: 'in_file', 'op_string'
# output: 'out_file'
)
mn_water_scaled = Node(
interface=ImageMaths(suffix="_scaled"),
name='water_scaled',
iterfield=['in_file']
# inputs: 'in_file', 'op_string'
# output: 'out_file'
)
if n4:
wf.connect([
(mn_n4_fat, mn_fat_scaled, [('output_image', 'in_file')]),
(mn_n4_water, mn_water_scaled, [('output_image', 'in_file')]),
(mn_fat_stats, mn_fat_scaled, [(('out_stat', scale), 'op_string')]),
(mn_water_stats, mn_water_scaled, [(('out_stat', scale), 'op_string')])
])
else:
wf.connect([
(n_selectfiles, mn_fat_scaled, [('fat_composed', 'in_file')]),
(n_selectfiles, mn_water_scaled, [('water_composed', 'in_file')]),
(mn_fat_stats, mn_fat_scaled, [(('out_stat', scale), 'op_string')]),
(mn_water_stats, mn_water_scaled, [(('out_stat', scale), 'op_string')])
])
# fatsegnet could work here when running on cluster, but in multiproc memory issues on GPU
# mn_fatsegnet = MapNode(
# interface=fatsegnet.FatSegNetInterface(
# out_suffix='/afm02/Q2/Q2653/data/2021-01-18-fatsegnet-output/out_5'
# ),
# iterfield=['water_file', 'fat_file'],
# name='fatsegnet'
# # output: 'out_file'
# )
# wf.connect([
# (mn_fat_scaled, mn_fatsegnet, [('out_file', 'fat_file')]),
# (mn_water_scaled, mn_fatsegnet, [('out_file', 'water_file')]),
# ])
# datasink
n_datasink_fat = Node(
interface=DataSink(base_directory=bids_dir,
container=out_dir,
parameterization=True,
substitutions=[('_subject_id_', '')],
regexp_substitutions=[('sub-\w{5}_t1.*', 'FatImaging_F.nii.gz')]),
name='datasink_fat'
)
n_datasink_water = Node(
interface=DataSink(base_directory=bids_dir,
container=out_dir,
parameterization=True,
substitutions=[('_subject_id_', '')],
regexp_substitutions=[('sub-\w{5}_t1.*', 'FatImaging_W.nii.gz')]),
name='datasink_water'
)
# https://pythex.org/: search for sub-, then 5 numbers then _t1 and grab the rest
wf.connect([
(mn_fat_scaled, n_datasink_fat, [('out_file', 'preprocessed_mul4.@fat')]),
(mn_water_scaled, n_datasink_water, [('out_file', 'preprocessed_mul4.@water')]),
])
# https://nipype.readthedocs.io/en/0.11.0/users/grabbing_and_sinking.html
# https://miykael.github.io/nipype_tutorial/notebooks/example_1stlevel.html
# The period (.) indicates that a subfolder should be created.
# But if we wanted to store it in the same folder,
# we would use the .@ syntax. The @ tells the DataSink interface to not create the subfolder.
return wf
<< << << < HEAD
== == == =
>>>>>> > e5874a2... BUG Fixed CEST workflow
backg_fit = Node(LtzWaterMT(sequence=sequence, verbose=True),
name='backg_fit')
# Simulate data for all frequencies
sequence['MTSat']['sat_f0'] = zfrqs.tolist()
sequence['MTSat']['sat_angle'] = np.repeat(180.0, len(zfrqs)).tolist()
backg_sim = Node(LtzWaterMTSim(sequence=sequence,
noise=0,
out_file='backg_sim.nii.gz',
verbose=True),
name='backg_sim')
backg_sub = Node(ImageMaths(op_string='-sub',
out_file='no_backg_sub.nii.gz'),
name='backg_sub', iterfield=['in_file'])
f0_indices = (np.abs(zfrqs) > 0.99) & (np.abs(zfrqs) < 10.1)
sequence['MTSat']['sat_f0'] = zfrqs[f0_indices].tolist()
sequence['MTSat']['sat_angle'] = np.repeat(
180.0, len(f0_indices)).tolist()
an_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(), out_file='fg_zspec.nii.gz'),
name='an_select')
<< << << < HEAD
an_fit = Node(LamideFit(sequence=sequence,
Zref=0.0,
additive=True,
verbose=True),
== == == =
datasink.inputs.container = output_dir
# DataSink Substitutions
substitutions = [('_subject_id', ''), ('_subject','subject'), # Substitutions have an order!!!
('_in_matrix_file_', ''), # Turning a node into an iterable defaults to naming the output file to input variable name
('%s' % outpath_mat.replace('/','..'), ''), # When creating own nodes, output files are (by default) named according to the absolute path, however Nipype replaces '/' with '..' to avoid creating directories. It's ugly. This is my 'make-do' workaround.
('.mat', ''),
('_voxel_size_','vox_dims_'),
('anat_flirt','anat_tform'), # Output files are (by default) named according to the input function or variable name. Each additional node will add '_functionname'. Be careful when creating own nodes. Nipype gets confused. Overwritten or misrecognised in 'processing' folder.
('anat_resample','anat_rsmpl'),
('_var_','var_')
]
datasink.inputs.substitutions = substitutions
# Smooth
smooth = Node(ImageMaths(op_string='-fmean -s 2'),
name="smooth")
smooth_spm = Node(Smooth(fwhm=smoothing_size),
name="smooth")
# Resample
resample = Node(Resample(outputtype='NIFTI',
resample_mode='Li'),
name="resample")
resample.iterables = ('voxel_size', vox_lst(min_dim,max_dim,step_dim)) # Example of turning a node (function) into an iterable, e.g. nodename.iterables = ('parameter',list_of_iterables). Depending on parameter, list may need to be tuple, etc.
# Noise
noise = Node(interface=Function(input_names=['base_dir','output_dir','in_file','var'], # Self-created node. Needs improvement.
output_names=['out_file'],
function=snr_img),
name="noise")
def group_onesample_openfmri(dataset_dir,
model_id=None,
task_id=None,
l1output_dir=None,
out_dir=None,
no_reversal=False):
wk = Workflow(name='one_sample')
wk.base_dir = os.path.abspath(work_dir)
info = Node(
util.IdentityInterface(fields=['model_id', 'task_id', 'dataset_dir']),
name='infosource')
info.inputs.model_id = model_id
info.inputs.task_id = task_id
info.inputs.dataset_dir = dataset_dir
num_copes = contrasts_num(model_id, task_id, dataset_dir)
dg = Node(DataGrabber(infields=['model_id', 'task_id', 'cope_id'],
outfields=['copes', 'varcopes']),
name='grabber')
dg.inputs.template = os.path.join(
l1output_dir, 'model%03d/task%03d/*/%scopes/mni/%scope%02d.nii.gz')
dg.inputs.template_args['copes'] = [[
'model_id', 'task_id', '', '', 'cope_id'
]]
dg.inputs.template_args['varcopes'] = [[
'model_id', 'task_id', 'var', 'var', 'cope_id'
]]
dg.iterables = ('cope_id', num_copes)
dg.inputs.sort_filelist = True
wk.connect(info, 'model_id', dg, 'model_id')
wk.connect(info, 'task_id', dg, 'task_id')
model = Node(L2Model(), name='l2model')
wk.connect(dg, ('copes', get_len), model, 'num_copes')
mergecopes = Node(Merge(dimension='t'), name='merge_copes')
wk.connect(dg, 'copes', mergecopes, 'in_files')
mergevarcopes = Node(Merge(dimension='t'), name='merge_varcopes')
wk.connect(dg, 'varcopes', mergevarcopes, 'in_files')
mask_file = fsl.Info.standard_image('MNI152_T1_2mm_brain_mask.nii.gz')
flame = Node(FLAMEO(), name='flameo')
flame.inputs.mask_file = mask_file
flame.inputs.run_mode = 'flame1'
wk.connect(model, 'design_mat', flame, 'design_file')
wk.connect(model, 'design_con', flame, 't_con_file')
wk.connect(mergecopes, 'merged_file', flame, 'cope_file')
wk.connect(mergevarcopes, 'merged_file', flame, 'var_cope_file')
wk.connect(model, 'design_grp', flame, 'cov_split_file')
smoothest = Node(SmoothEstimate(), name='smooth_estimate')
wk.connect(flame, 'zstats', smoothest, 'zstat_file')
smoothest.inputs.mask_file = mask_file
cluster = Node(Cluster(), name='cluster')
wk.connect(smoothest, 'dlh', cluster, 'dlh')
wk.connect(smoothest, 'volume', cluster, 'volume')
cluster.inputs.connectivity = 26
cluster.inputs.threshold = 2.3
cluster.inputs.pthreshold = 0.05
cluster.inputs.out_threshold_file = True
cluster.inputs.out_index_file = True
cluster.inputs.out_localmax_txt_file = True
wk.connect(flame, 'zstats', cluster, 'in_file')
ztopval = Node(ImageMaths(op_string='-ztop', suffix='_pval'),
name='z2pval')
wk.connect(flame, 'zstats', ztopval, 'in_file')
sinker = Node(DataSink(), name='sinker')
sinker.inputs.base_directory = os.path.abspath(out_dir)
sinker.inputs.substitutions = [('_cope_id', 'contrast'),
('_maths__', '_reversed_')]
wk.connect(flame, 'zstats', sinker, 'stats')
wk.connect(cluster, 'threshold_file', sinker, 'stats.@thr')
wk.connect(cluster, 'index_file', sinker, 'stats.@index')
wk.connect(cluster, 'localmax_txt_file', sinker, 'stats.@localmax')
if no_reversal == False:
zstats_reverse = Node(BinaryMaths(), name='zstats_reverse')
zstats_reverse.inputs.operation = 'mul'
zstats_reverse.inputs.operand_value = -1
wk.connect(flame, 'zstats', zstats_reverse, 'in_file')
cluster2 = cluster.clone(name='cluster2')
wk.connect(smoothest, 'dlh', cluster2, 'dlh')
wk.connect(smoothest, 'volume', cluster2, 'volume')
wk.connect(zstats_reverse, 'out_file', cluster2, 'in_file')
ztopval2 = ztopval.clone(name='ztopval2')
wk.connect(zstats_reverse, 'out_file', ztopval2, 'in_file')
wk.connect(zstats_reverse, 'out_file', sinker, 'stats.@neg')
wk.connect(cluster2, 'threshold_file', sinker, 'stats.@neg_thr')
wk.connect(cluster2, 'index_file', sinker, 'stats.@neg_index')
wk.connect(cluster2, 'localmax_txt_file', sinker,
'stats.@neg_localmax')
return wk
os.chdir(experiment_dir + '/' + sub)
#location/directory containing all the data for this study/subject
ae = amico.Evaluation(experiment_dir, sub)
#load data
if amico_model == "NODDI":
mask_file = "data_brain_mask.nii.gz"
# generate scheme file from the bvals/bvecs
amico.util.fsl2scheme('data.bval', 'data.bvec')
amico_dir = opj(experiment_dir, sub, amico_model)
if not os.path.exists(amico_dir):
os.mkdir(amico_dir)
os.rename('data.scheme', amico_dir + '/noddi.scheme')
if amico_model == "CylinderZeppelinBall":
threshL = ImageMaths(op_string='-thr 2 -uthr 2')
threshL.inputs.in_file = experiment_dir + sub + '/aseg_trans.nii.gz'
threshL.inputs.out_file = experiment_dir + sub + '/wmL_mask.nii.gz'
threshL.run()
threshR = ImageMaths(op_string='-thr 41 -uthr 41')
threshR.inputs.in_file = experiment_dir + sub + '/aseg_trans.nii.gz'
threshR.inputs.out_file = experiment_dir + sub + '/wmR_mask.nii.gz'
threshR.run()
add_string = '-add ' + experiment_dir + sub + '/wmR_mask.nii.gz'
wm = ImageMaths(op_string=add_string)
wm.inputs.in_file = experiment_dir + sub + '/wmL_mask.nii.gz'
wm.inputs.out_file = experiment_dir + sub + '/wm_mask.nii.gz'
wm.run()
mask_file = "wm_mask.nii.gz"
os.remove('wmR_mask.nii.gz')
os.remove('wmL_mask.nii.gz')
binarizeDilatedCompleteMask = Node(Binarize(min=0.1, binary_file='dilated_complete_mask.nii'),
name='binarizeDilatedCompleteMask')
applyVolTrans_cortical_mask = Node(ApplyVolTransform(reg_header=True,
interp='nearest'),
name='applyVolTrans_cortical_mask')
applyVolTrans_brain_mask = Node(ApplyVolTransform(reg_header=True,
interp='nearest'),
name='applyVolTrans_brain_mask')
applyVolTrans_complete_mask = Node(ApplyVolTransform(reg_header=True,
interp='nearest'),
name='applyVolTrans_complete_mask')
aparc_robust_BET_mask = MapNode(interface=ImageMaths(suffix='_ribbon_robust_BET',
op_string='-mas', output_type='NIFTI', out_file='aparc_robust_BET.nii'),
iterfield=['in_file'],
name='aparc_robust_BET_mask')
# Create the mask pipeline
preproc_ALPACA_maskflow = Workflow(name='prepro_ALPACA_maskflow')
# Connect all components of the preprocessing workflow - aparc / ribbon mask
preproc_ALPACA_maskflow.connect([(realign, meanfuncmask, [('mean_image', 'in_file')]), # create a skull stripped mask image from the mean functional
(binarizebrainmask, mriconvert_brain_mask, [('binary_file', 'in_file')]), # convert brainmask to nifti
(mriconvert_brain_mask, applyVolTrans_brain_mask, [('out_file', 'source_file')]), # transform brainmask to functional space
(realign, applyVolTrans_brain_mask, [('mean_image', 'target_file')]),
(applyVolTrans_brain_mask, dilate_brain_mask, [('transformed_file', 'in_file')]), # dilate transformed brainmask
(dilate_brain_mask, binarizeDilatedBrainMask, [('binary_file', 'in_file')]), # binarize dilated and transformed brainmask
(binarizeCortical, wholebrainmask, [('binary_file','in_file')]),
(binarizeSubcortical, wholebrainmask, [('binary_file', 'operand_file')]), # combine aparc_aseg and ribbon files to get a whole brain mask
def canonical(subjects_participants, regdir, f2s,
template = "~/GitHub/mriPipeline/templates/waxholm/WHS_SD_rat_T2star_v1.01_downsample3.nii.gz",
f_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
):
"""Warp a functional image based on the functional-to-structural and the structural-to-template registrations.
Currently this approach is failing because the functiona-to-structural registration pushes the brain stem too far down.
This may be
"""
template = os.path.expanduser(template)
for subject_participant in subjects_participants:
func_image_dir = os.path.expanduser(f_file_format.format(**subject_participant))
struct_image_dir = os.path.expanduser(s_file_format.format(**subject_participant))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir,myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir,myfile)
except FileNotFoundError:
pass
else:
#struct
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200,200,200,200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}/ss_n4_{}_ofM{}.nii.gz'.format(regdir,participant,i)
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500,500,500,500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}/ss__n4_{}_ofM{}.nii.gz'.format(regdir,participant,i)
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET_res = struct_BET.run()
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0,), (1.0, 3.0, 5.0)] ##
struct_registration.inputs.number_of_iterations = [[2000, 1000, 500], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11, 1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1], [4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1],[3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [True, True]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = 6
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}/s_{}_ofM{}.nii.gz'.format(regdir,participant,i)
struct_registration_res = struct_registration.run()
#func
func_n4 = ants.N4BiasFieldCorrection()
func_n4.inputs.dimension = 3
func_n4.inputs.input_image = func_image
func_n4.inputs.bspline_fitting_distance = 100
func_n4.inputs.shrink_factor = 2
func_n4.inputs.n_iterations = [200,200,200,200]
func_n4.inputs.convergence_threshold = 1e-11
func_n4.inputs.output_image = '{}/f_n4_{}_ofM{}.nii.gz'.format(regdir,participant,i)
func_n4_res = func_n4.run()
func_registration = ants.Registration()
func_registration.inputs.fixed_image = n4_res.outputs.output_image
func_registration.inputs.output_transform_prefix = "func_"
func_registration.inputs.transforms = [f2s]
func_registration.inputs.transform_parameters = [(0.1,)]
func_registration.inputs.number_of_iterations = [[40, 20, 10]]
func_registration.inputs.dimension = 3
func_registration.inputs.write_composite_transform = True
func_registration.inputs.collapse_output_transforms = True
func_registration.inputs.initial_moving_transform_com = True
func_registration.inputs.metric = ['MeanSquares']
func_registration.inputs.metric_weight = [1]
func_registration.inputs.radius_or_number_of_bins = [16]
func_registration.inputs.sampling_strategy = ["Regular"]
func_registration.inputs.sampling_percentage = [0.3]
func_registration.inputs.convergence_threshold = [1.e-2]
func_registration.inputs.convergence_window_size = [8]
func_registration.inputs.smoothing_sigmas = [[4, 2, 1]] # [1,0.5,0]
func_registration.inputs.sigma_units = ['vox']
func_registration.inputs.shrink_factors = [[3, 2, 1]]
func_registration.inputs.use_estimate_learning_rate_once = [True]
func_registration.inputs.use_histogram_matching = [False]
func_registration.inputs.winsorize_lower_quantile = 0.005
func_registration.inputs.winsorize_upper_quantile = 0.995
func_registration.inputs.args = '--float'
func_registration.inputs.num_threads = 6
func_registration.inputs.moving_image = func_n4_res.outputs.output_image
func_registration.inputs.output_warped_image = '{}/f_{}_ofM{}.nii.gz'.format(regdir,participant,i)
func_registration_res = func_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False, False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}/{}_ofM{}.nii.gz'.format(regdir,participant,i)
warp.num_threads = 6
warp.inputs.input_image = func_image
warp.inputs.transforms = [func_registration_res.outputs.composite_transform, struct_registration_res.outputs.composite_transform]
warp.run()
# <editor-fold desc="Scale phase data">
stats = MapNode(ImageStats(op_string='-R'),
name='stats_node',
iterfield=['in_file'])
def scale_to_pi(min_and_max):
data_min = min_and_max[0][0]
data_max = min_and_max[0][1]
# TODO: Test at 3T with -4096 to + 4096 range
return '-add %.10f -div %.10f -mul 6.28318530718 -sub 3.14159265359' % (
data_min, data_max + data_min)
phs_range_n = MapNode(ImageMaths(),
name='phs_range_node',
iterfield=['in_file'])
wf.connect([(selectfiles, stats, [('phs', 'in_file')]),
(selectfiles, phs_range_n, [('phs', 'in_file')]),
(stats, phs_range_n, [(('out_stat', scale_to_pi), 'op_string')])])
# </editor-fold>
# <editor-fold desc="Read echotime and fieldstrenghts from json files ">
def read_json(in_file):
import os
te = 0.001
b0 = 7
def structural_per_participant_test(
participant,
conditions=["", "_aF", "_cF1", "_cF2", "_pF"],
template="/home/chymera/ni_data/templates/ds_QBI_chr.nii.gz",
):
for i in conditions:
image_dir = "/home/chymera/ni_data/ofM.dr/preprocessing/generic_work/_subject_session_{}.ofM{}/_scan_type_T2_TurboRARE/s_bru2nii/".format(
participant, i)
print(image_dir)
try:
for myfile in os.listdir(image_dir):
if myfile.endswith(".nii"):
mimage = os.path.join(image_dir, myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = mimage
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = 'ss_n4_{}_ofM{}.nii.gz'.format(
participant, i)
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = mimage
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500, 500, 500, 500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = 'ss__n4_{}_ofM{}.nii.gz'.format(
participant, i)
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET_res = struct_BET.run()
mask = ApplyMask()
mask.inputs.in_file = n4_res.outputs.output_image
mask.inputs.mask_file = struct_BET_res.outputs.mask_file
mask_res = mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Rigid', 'Affine',
'SyN'] ##
struct_registration.inputs.transform_parameters = [(.1, ), (1.0, ),
(1.0, 3.0, 5.0)
] ##
struct_registration.inputs.number_of_iterations = [[
150, 100, 50
], [2000, 1000, 500], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = [
'MeanSquares', 'MeanSquares', 'Mattes'
]
struct_registration.inputs.metric_weight = [1, 1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 16,
32] #
struct_registration.inputs.sampling_strategy = [
'Random', 'Random', None
]
struct_registration.inputs.sampling_percentage = [0.3, 0.3, 0.3]
struct_registration.inputs.convergence_threshold = [
1.e-10, 1.e-11, 1.e-8
] #
struct_registration.inputs.convergence_window_size = [20, 20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2,
1], [4, 2, 1],
[4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1],
[3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [
True, True, True
]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [
False, False, False
]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = 6
struct_registration.inputs.moving_image = mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = 'ss_{}_ofM{}.nii.gz'.format(
participant, i)
res = struct_registration.run()
####################
## ants_brain_ext ##
####################
ants_be_n = MapNode(BrainExtraction(dimension=3, brain_template='/data/fasttemp/uqtshaw/tomcat/data/derivatives/myelin_mapping/T_template.nii.gz', brain_probability_mask='/data/fasttemp/uqtshaw/tomcat/data/derivatives/myelin_mapping/T_template_BrainCerebellumProbabilityMask.nii.gz'),
name='ants_be_node', iterfield=['anatomical_image'])
wf.connect([(selectfiles, ants_be_n, [('t1w', 'anatomical_image')])])
############
## antsCT ##
############
antsct_n = MapNode(CorticalThickness(dimension=3, brain_template='/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/T_template.nii.gz', brain_probability_mask='/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/T_template_BrainCerebellumProbabilityMask.nii.gz', segmentation_priors=['/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/Priors/priors1.nii.gz', '/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/Priors/priors2.nii.gz', '/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/Priors/priors3.nii.gz', '/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/Priors/priors4.nii.gz', '/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/Priors/priors5.nii.gz'], t1_registration_template='/data/fastertemp/uqtshaw/ANTS/ants_ct_templates/T_template_BrainCerebellum.nii.gz'),
name='ants_node', iterfield=['anatomical_image'])
wf.connect([(selectfiles, antsct_n, [('t1w', 'anatomical_image')])])
###############
## mult_mask ##
###############
mult_mask_n_flair = MapNode(ImageMaths(op_string='-mul'),
name="mult_mask_flair", iterfield=['in_file', 'in_file2'])
wf.connect([(ants_be_n, mult_mask_n_flair, [('BrainExtractionMask', 'in_file')])])
wf.connect([(flirt_n_flair, mult_mask_n_flair, [('out_file', 'in_file2')])])
mult_mask_n_space = MapNode(ImageMaths(op_string='-mul'),
name="mult_mask_space", iterfield=['in_file', 'in_file2'])
wf.connect([(ants_be_n, mult_mask_n_space, [('BrainExtractionMask', 'in_file')])])
wf.connect([(flirt_n_space, mult_mask_n_space, [('out_file', 'in_file2')])])
###############
## N4 the T2 ##
###############
n4_n_flair = MapNode(N4BiasFieldCorrection(dimension=3, bspline_fitting_distance=300, shrink_factor=3, n_iterations=[50,50,30,20]),
name="n4_flair", iterfield=['input_image'])
wf.connect([(mult_mask_n_flair, n4_n_flair, [('out_file', 'input_image')])])
n4_n_space = MapNode(N4BiasFieldCorrection(dimension=3, bspline_fitting_distance=300, shrink_factor=3, n_iterations=[50,50,30,20]),
name="n4_space", iterfield=['input_image'])
def amide_noe(zfrqs, name='Amide_NOE'):
inputnode = Node(IdentityInterface(fields=['zspec_file', 'mask_file']),
name='inputnode')
outputnode = Node(
IdentityInterface(fields=['diff_file', 'DS', 'MT', 'Amide', 'NOE']),
name='outputnode')
# Repeat 2-pool fit
f0_indices = (np.abs(zfrqs) > 9.9) | (np.abs(zfrqs) < 1.1)
sequence = {
'MTSat': {
'pulse': {
'p1': 0.4,
'p2': 0.3,
'bandwidth': 0.39
},
'Trf': 0.02,
'TR': 4,
'FA': 5,
'sat_f0': zfrqs[f0_indices].tolist(),
'sat_angle': np.repeat(180.0, len(f0_indices)).tolist()
}
}
two_pools = [{
'name': 'DS',
'df0': [0, -2.5, 2.5],
'fwhm': [1.0, 1.e-6, 3.0],
'A': [0.2, 1.e-3, 1.0],
'use_bandwidth': True
}, {
'name': 'MT',
'df0': [-2.5, -5.0, -0.5],
'fwhm': [50.0, 35.0, 200.0],
'A': [0.3, 1.e-3, 1.0]
}]
backg_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(),
out_file='bg_zspec.nii.gz'),
name='backg_select')
backg_fit = Node(Lorentzian(sequence=sequence,
pools=two_pools,
verbose=True),
name='backg_fit')
# Simulate data for all frequencies
sequence['MTSat']['sat_f0'] = zfrqs.tolist()
sequence['MTSat']['sat_angle'] = np.repeat(180.0, len(zfrqs)).tolist()
backg_sim = Node(LorentzianSim(sequence=sequence,
pools=two_pools,
noise=0,
in_file='backg_sim.nii.gz',
verbose=True),
name='backg_sim')
backg_sub = Node(ImageMaths(op_string='-sub',
out_file='no_backg_sub.nii.gz'),
name='backg_sub')
an_pools = [{
'name': 'Amide',
'df0': [3.5, 2.0, 6.0],
'fwhm': [2.0, 0.4, 4.0],
'A': [0.2, 1.e-3, 0.2],
'use_bandwidth': True
}, {
'name': 'NOE',
'df0': [-4.0, -6.0, -2.0],
'fwhm': [2.0, 0.4, 4.0],
'A': [0.2, 1.e-3, 0.2],
'use_bandwidth': True
}]
f0_indices = (np.abs(zfrqs) > 0.99) & (np.abs(zfrqs) < 10.1)
sequence['MTSat']['sat_f0'] = zfrqs[f0_indices].tolist()
sequence['MTSat']['sat_angle'] = np.repeat(180.0, len(f0_indices)).tolist()
an_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(),
out_file='fg_zspec.nii.gz'),
name='an_select')
an_fit = Node(Lorentzian(sequence=sequence,
pools=an_pools,
Zref=0.0,
additive=True,
verbose=True),
name='an_pool')
outputnode = Node(IdentityInterface(
fields=['zspec', 'f0_map', 'mask', 'DS', 'MT', 'Amide', 'NOE']),
name='outputnode')
wf = Workflow(name=name)
wf.connect([
(inputnode, backg_select, [('zspec_file', 'in_file')]),
(backg_select, backg_fit, [('out_file', 'in_file')]),
(inputnode, backg_fit, [('mask_file', 'mask_file')]),
(backg_fit, backg_sim, [('DS_f0', 'DS_f0'), ('DS_fwhm', 'DS_fwhm'),
('DS_A', 'DS_A'), ('MT_f0', 'MT_f0'),
('MT_fwhm', 'MT_fwhm'), ('MT_A', 'MT_A')]),
(inputnode, backg_sub, [('zspec_file', 'in_file2')]),
(backg_sim, backg_sub, [('out_file', 'in_file')]),
(backg_sub, an_select, [('out_file', 'in_file')]),
(an_select, an_fit, [('out_file', 'in_file')]),
(inputnode, an_fit, [('mask_file', 'mask_file')]),
(backg_sub, outputnode, [('out_file', 'diff_file')]),
(backg_fit, outputnode, [('DS_A', 'DS'), ('MT_A', 'MT')]),
(an_fit, outputnode, [('Amide_A', 'Amide'), ('NOE_A', 'NOE')])
])
return wf
def structural_to_functional_per_participant_test(
subjects_sessions,
template="~/GitHub/mriPipeline/templates/waxholm/new/WHS_SD_masked.nii.gz",
f_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
num_threads=3,
):
template = os.path.expanduser(template)
for subject_session in subjects_sessions:
func_image_dir = os.path.expanduser(
f_file_format.format(**subject_session))
struct_image_dir = os.path.expanduser(
s_file_format.format(**subject_session))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir, myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir, myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}_{}_1_biasCorrection_forRegistration.nii.gz'.format(
*subject_session.values())
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500, 500, 500, 500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}_{}_1_biasCorrection_forMasking.nii.gz'.format(
*subject_session.values())
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET.inputs.out_file = '{}_{}_2_brainExtraction.nii.gz'.format(
*subject_session.values())
struct_BET_res = struct_BET.run()
# we need/can not apply a fill, because the "holes" if any, will be at the rostral edge (touching it, and thus not counting as holes)
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask.inputs.out_file = '{}_{}_3_brainMasked.nii.gz'.format(
*subject_session.values())
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0, ),
(1.0, 3.0, 5.0)
] ##
struct_registration.inputs.number_of_iterations = [[
2000, 1000, 500
], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11,
1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1],
[4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [
True, True
]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = num_threads
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}_{}_4_structuralRegistration.nii.gz'.format(
*subject_session.values())
struct_registration_res = struct_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}_{}_5_functionalWarp.nii.gz'.format(
*subject_session.values())
warp.num_threads = num_threads
warp.inputs.input_image = func_image
warp.inputs.transforms = struct_registration_res.outputs.composite_transform
warp.run()
def prep(zfrqs, dummies=0, pca_retain=0, name='CEST_prep'):
inputnode = Node(IdentityInterface(fields=['zspec_file', 'ref_file']),
name='inputnode')
outputnode = Node(IdentityInterface(
fields=['zspec_file', 'f0_map', 'mask_file', 'ref_file', 'DS', 'MT']),
name='outputnode')
moco = Node(MCFLIRT(cost='mutualinfo', mean_vol=True), name='moco')
mask = Node(BET(mask=True, no_output=True), name='mask')
if (dummies > 0):
ref_index = dummies - 1
zspec_select = Node(Select(volumes=list(range(dummies, len(zfrqs))),
out_file='zspec.nii.gz'),
name='zspec_select')
zfrqs = np.array(zfrqs[dummies:])
else:
ref_index = 0
zfrqs = np.array(zfrqs)
zspec_ref = Node(Select(volumes=[
ref_index,
], out_file='reference.nii.gz'),
name='zspec_ref')
zspec_norm = Node(ImageMaths(op_string='-div', out_file='zspec.nii.gz'),
name='zspec_norm')
f0_indices = (np.abs(zfrqs) > 7) | (np.abs(zfrqs) < 1.1)
sat_frqs = zfrqs[f0_indices]
sat_angles = np.repeat(180.0, len(f0_indices))
f0_select = Node(Select(volumes=np.where(f0_indices)[0].tolist(),
out_file='background_zspec.nii.gz'),
name='f0_select')
sequence = {
'MTSat': {
'pulse': {
'p1': 0.4,
'p2': 0.3,
'bandwidth': 0.39
},
'Trf': 0.02,
'TR': 4,
'FA': 5,
'sat_f0': sat_frqs.tolist(),
'sat_angle': sat_angles.tolist()
}
}
two_pools = [{
'name': 'DS',
'df0': [0, -2.5, 2.5],
'fwhm': [1.0, 1.e-6, 3.0],
'A': [0.2, 1.e-3, 1.0],
'use_bandwidth': True
}, {
'name': 'MT',
'df0': [-2.5, -5.0, -0.5],
'fwhm': [50.0, 35.0, 200.0],
'A': [0.3, 1.e-3, 1.0]
}]
f0_fit = Node(Lorentzian(sequence=sequence, pools=two_pools, verbose=True),
name='f0_fit')
out_frqs = np.sort(zfrqs)
f0_correct = Node(ZSpec(in_freqs=zfrqs.tolist(),
out_freqs=out_frqs.tolist(),
verbose=True),
name='f0_correct')
prep = Workflow(name=name)
prep.connect([(inputnode, moco, [('zspec_file', 'in_file'),
('ref_file', 'ref_file')]),
(moco, zspec_ref, [('out_file', 'in_file')]),
(moco, mask, [('mean_img', 'in_file')]),
(zspec_ref, zspec_norm, [('out_file', 'in_file2')]),
(zspec_norm, f0_select, [('out_file', 'in_file')]),
(f0_select, f0_fit, [('out_file', 'in_file')]),
(mask, f0_fit, [('mask_file', 'mask_file')]),
(zspec_norm, f0_correct, [('out_file', 'in_file')]),
(f0_fit, f0_correct, [('DS_f0', 'f0_map')]),
(mask, f0_correct, [('mask_file', 'mask_file')]),
(moco, outputnode, [('mean_img', 'ref_file')]),
(mask, outputnode, [('out_file', 'mask_file')]),
(f0_fit, outputnode, [('DS_f0', 'f0_map'), ('DS_A', 'DS'),
('MT_A', 'MT')])])
if (dummies > 0):
prep.connect([(moco, zspec_select, [('out_file', 'in_file')]),
(zspec_select, zspec_norm, [('out_file', 'in_file')])])
else:
prep.connect([(moco, zspec_norm, [('out_file', 'in_file')])])
if pca_retain > 0:
f0_pca = Node(PCA(retain=pca_retain, projections_file='proj.nii.gz'),
name='f0_pca')
prep.connect([(f0_correct, f0_pca, [('out_file', 'in_file')]),
(f0_pca, outputnode, [('out_file', 'zspec_file')])])
else:
prep.connect([(f0_correct, outputnode, [('out_file', 'zspec_file')])])
return (prep, out_frqs)
def group_multregress_openfmri(dataset_dir,
model_id=None,
task_id=None,
l1output_dir=None,
out_dir=None,
no_reversal=False,
plugin=None,
plugin_args=None,
flamemodel='flame1',
nonparametric=False,
use_spm=False):
meta_workflow = Workflow(name='mult_regress')
meta_workflow.base_dir = work_dir
for task in task_id:
task_name = get_taskname(dataset_dir, task)
cope_ids = l1_contrasts_num(model_id, task_name, dataset_dir)
regressors_needed, contrasts, groups, subj_list = get_sub_vars(
dataset_dir, task_name, model_id)
for idx, contrast in enumerate(contrasts):
wk = Workflow(name='model_%03d_task_%03d_contrast_%s' %
(model_id, task, contrast[0][0]))
info = Node(util.IdentityInterface(
fields=['model_id', 'task_id', 'dataset_dir', 'subj_list']),
name='infosource')
info.inputs.model_id = model_id
info.inputs.task_id = task
info.inputs.dataset_dir = dataset_dir
dg = Node(DataGrabber(infields=['model_id', 'task_id', 'cope_id'],
outfields=['copes', 'varcopes']),
name='grabber')
dg.inputs.template = os.path.join(
l1output_dir,
'model%03d/task%03d/%s/%scopes/%smni/%scope%02d.nii%s')
if use_spm:
dg.inputs.template_args['copes'] = [[
'model_id', 'task_id', subj_list, '', 'spm/', '',
'cope_id', ''
]]
dg.inputs.template_args['varcopes'] = [[
'model_id', 'task_id', subj_list, 'var', 'spm/', 'var',
'cope_id', '.gz'
]]
else:
dg.inputs.template_args['copes'] = [[
'model_id', 'task_id', subj_list, '', '', '', 'cope_id',
'.gz'
]]
dg.inputs.template_args['varcopes'] = [[
'model_id', 'task_id', subj_list, 'var', '', 'var',
'cope_id', '.gz'
]]
dg.iterables = ('cope_id', cope_ids)
dg.inputs.sort_filelist = False
wk.connect(info, 'model_id', dg, 'model_id')
wk.connect(info, 'task_id', dg, 'task_id')
model = Node(MultipleRegressDesign(), name='l2model')
model.inputs.groups = groups
model.inputs.contrasts = contrasts[idx]
model.inputs.regressors = regressors_needed[idx]
mergecopes = Node(Merge(dimension='t'), name='merge_copes')
wk.connect(dg, 'copes', mergecopes, 'in_files')
if flamemodel != 'ols':
mergevarcopes = Node(Merge(dimension='t'),
name='merge_varcopes')
wk.connect(dg, 'varcopes', mergevarcopes, 'in_files')
mask_file = fsl.Info.standard_image(
'MNI152_T1_2mm_brain_mask.nii.gz')
flame = Node(FLAMEO(), name='flameo')
flame.inputs.mask_file = mask_file
flame.inputs.run_mode = flamemodel
#flame.inputs.infer_outliers = True
wk.connect(model, 'design_mat', flame, 'design_file')
wk.connect(model, 'design_con', flame, 't_con_file')
wk.connect(mergecopes, 'merged_file', flame, 'cope_file')
if flamemodel != 'ols':
wk.connect(mergevarcopes, 'merged_file', flame,
'var_cope_file')
wk.connect(model, 'design_grp', flame, 'cov_split_file')
if nonparametric:
palm = Node(Function(input_names=[
'cope_file', 'design_file', 'contrast_file', 'group_file',
'mask_file', 'cluster_threshold'
],
output_names=['palm_outputs'],
function=run_palm),
name='palm')
palm.inputs.cluster_threshold = 3.09
palm.inputs.mask_file = mask_file
palm.plugin_args = {
'sbatch_args': '-p om_all_nodes -N1 -c2 --mem=10G',
'overwrite': True
}
wk.connect(model, 'design_mat', palm, 'design_file')
wk.connect(model, 'design_con', palm, 'contrast_file')
wk.connect(mergecopes, 'merged_file', palm, 'cope_file')
wk.connect(model, 'design_grp', palm, 'group_file')
smoothest = Node(SmoothEstimate(), name='smooth_estimate')
wk.connect(flame, 'zstats', smoothest, 'zstat_file')
smoothest.inputs.mask_file = mask_file
cluster = Node(Cluster(), name='cluster')
wk.connect(smoothest, 'dlh', cluster, 'dlh')
wk.connect(smoothest, 'volume', cluster, 'volume')
cluster.inputs.connectivity = 26
cluster.inputs.threshold = 2.3
cluster.inputs.pthreshold = 0.05
cluster.inputs.out_threshold_file = True
cluster.inputs.out_index_file = True
cluster.inputs.out_localmax_txt_file = True
wk.connect(flame, 'zstats', cluster, 'in_file')
ztopval = Node(ImageMaths(op_string='-ztop', suffix='_pval'),
name='z2pval')
wk.connect(flame, 'zstats', ztopval, 'in_file')
sinker = Node(DataSink(), name='sinker')
sinker.inputs.base_directory = os.path.join(
out_dir, 'task%03d' % task, contrast[0][0])
sinker.inputs.substitutions = [('_cope_id', 'contrast'),
('_maths_', '_reversed_')]
wk.connect(flame, 'zstats', sinker, 'stats')
wk.connect(cluster, 'threshold_file', sinker, 'stats.@thr')
wk.connect(cluster, 'index_file', sinker, 'stats.@index')
wk.connect(cluster, 'localmax_txt_file', sinker, 'stats.@localmax')
if nonparametric:
wk.connect(palm, 'palm_outputs', sinker, 'stats.palm')
if not no_reversal:
zstats_reverse = Node(BinaryMaths(), name='zstats_reverse')
zstats_reverse.inputs.operation = 'mul'
zstats_reverse.inputs.operand_value = -1
wk.connect(flame, 'zstats', zstats_reverse, 'in_file')
cluster2 = cluster.clone(name='cluster2')
wk.connect(smoothest, 'dlh', cluster2, 'dlh')
wk.connect(smoothest, 'volume', cluster2, 'volume')
wk.connect(zstats_reverse, 'out_file', cluster2, 'in_file')
ztopval2 = ztopval.clone(name='ztopval2')
wk.connect(zstats_reverse, 'out_file', ztopval2, 'in_file')
wk.connect(zstats_reverse, 'out_file', sinker, 'stats.@neg')
wk.connect(cluster2, 'threshold_file', sinker,
'stats.@neg_thr')
wk.connect(cluster2, 'index_file', sinker, 'stats.@neg_index')
wk.connect(cluster2, 'localmax_txt_file', sinker,
'stats.@neg_localmax')
meta_workflow.add_nodes([wk])
return meta_workflow
def init_mpm_wf(me_params, mtsat_params):
inputnode = Node(IdentityInterface(fields=[
'PDw_file', 'T1w_file', 'MTw_file', 'PDw_cal', 'T1w_cal', 'MTw_cal',
'B1_map'
]),
name='inputnode')
outputnode = Node(
IdentityInterface(fields=['PD_map', 'R1_map', 'R2s_map', 'mtsat_map']),
name='outputnode')
wf = Workflow(name='Multi-Parametric-Mapping')
bet = Node(BET(mask=True, no_output=True), name='brain_mask')
wf.connect([(inputnode, bet, [('T1w_file', 'in_file')])])
PD_B1minus = Node(B1Minus(), name='PD_B1minus')
t1_B1minus = Node(B1Minus(), name='t1_B1minus')
mt_B1minus = Node(B1Minus(), name='mt_B1minus')
wf.connect([(inputnode, PD_B1minus, [('PDw_cal', 'in_file')]),
(inputnode, t1_B1minus, [('T1w_cal', 'in_file')]),
(inputnode, mt_B1minus, [('MTw_cal', 'in_file')])])
pd0 = Node(Select(volumes=[
0,
], out_file='pd0.nii.gz'), name='pd0')
t10 = Node(Select(volumes=[
0,
], out_file='t10.nii.gz'), name='t10')
mt0 = Node(Select(volumes=[
0,
], out_file='mt0.nii.gz'), name='mt0')
wf.connect([(inputnode, pd0, [('PDw_file', 'in_file')]),
(inputnode, t10, [('T1w_file', 'in_file')]),
(inputnode, mt0, [('MTw_file', 'in_file')])])
PD_B1m_hires = Node(FLIRT(apply_xfm=True, uses_qform=True),
name='PD_B1m_hires')
t1_B1m_hires = Node(FLIRT(apply_xfm=True, uses_qform=True),
name='t1_B1m_hires')
mt_B1m_hires = Node(FLIRT(apply_xfm=True, uses_qform=True),
name='mt_B1m_hires')
wf.connect([(PD_B1minus, PD_B1m_hires, [('out_file', 'in_file')]),
(pd0, PD_B1m_hires, [('out_file', 'reference')]),
(t1_B1minus, t1_B1m_hires, [('out_file', 'in_file')]),
(t10, t1_B1m_hires, [('out_file', 'reference')]),
(mt_B1minus, mt_B1m_hires, [('out_file', 'in_file')]),
(mt0, mt_B1m_hires, [('out_file', 'reference')])])
pd_cal = Node(ImageMaths(op_string='-div'),
name='pd_cal',
iterfield=['in_file'])
t1_cal = Node(ImageMaths(op_string='-div'),
name='t1_cal',
iterfield=['in_file'])
mt_cal = Node(ImageMaths(op_string='-div'),
name='mt_cal',
iterfield=['in_file'])
wf.connect([(inputnode, pd_cal, [('PDw_file', 'in_file')]),
(PD_B1m_hires, pd_cal, [('out_file', 'in_file2')]),
(inputnode, t1_cal, [('T1w_file', 'in_file')]),
(t1_B1m_hires, t1_cal, [('out_file', 'in_file2')]),
(inputnode, mt_cal, [('MTw_file', 'in_file')]),
(mt_B1m_hires, mt_cal, [('out_file', 'in_file2')])])
t1_reg = Node(FLIRT(uses_qform=True, cost='mutualinfo'), name='t1_reg')
mt_reg = Node(FLIRT(uses_qform=True, cost='mutualinfo'), name='mt_reg')
t1_apply = Node(ApplyXfm4D(single_matrix=True), name='t1_apply')
mt_apply = Node(ApplyXfm4D(single_matrix=True), name='mt_apply')
wf.connect([(t10, t1_reg, [('out_file', 'in_file')]),
(pd0, t1_reg, [('out_file', 'reference')]),
(t1_cal, t1_apply, [('out_file', 'in_file')]),
(pd0, t1_apply, [('out_file', 'ref_vol')]),
(t1_reg, t1_apply, [('out_matrix_file', 'trans_file')]),
(mt0, mt_reg, [('out_file', 'in_file')]),
(pd0, mt_reg, [('out_file', 'reference')]),
(mt_cal, mt_apply, [('out_file', 'in_file')]),
(pd0, mt_apply, [('out_file', 'ref_vol')]),
(mt_reg, mt_apply, [('out_matrix_file', 'trans_file')])])
mpm = Node(MPMR2s(sequence=me_params, verbose=True), name='MPM_R2s')
mtsat = Node(MTSat(sequence=mtsat_params, verbose=True), name='MPM_MTSat')
wf.connect([(pd_cal, mpm, [('out_file', 'PDw_file')]),
(t1_apply, mpm, [('out_file', 'T1w_file')]),
(mt_apply, mpm, [('out_file', 'MTw_file')]),
(bet, mpm, [('mask_file', 'mask_file')]),
(mpm, mtsat, [('S0_PDw_map', 'PDw_file'),
('S0_T1w_map', 'T1w_file'),
('S0_MTw_map', 'MTw_file')]),
(inputnode, mtsat, [('B1_map', 'B1_map')]),
(bet, mtsat, [('mask_file', 'mask_file')]),
(mpm, outputnode, [('R2s_map', 'R2s_map')]),
(mtsat, outputnode, [('PD_map', 'PD_map'),
('R1_map', 'R1_map'),
('delta_map', 'mtsat_map')])])
return wf
import nipype.interfaces.fsl as fsl
from nipype.interfaces.fsl import ImageStats
from nipype.interfaces.fsl import ImageMaths
import numpy as np
from scipy import stats
sublist = range(101,123) # subject nr list
seglist = range(1,11) # range(1,11) nr of segments = (1 to 10) in this example there are 10 targets.
# make all the segments first
for i in sublist:
for j in seglist:
#get segment (note out_file contains L because this example is left striatum only)
ImageMaths(in_file=('ITC%sbig.nii.gz' % i), out_file=('%(1)s_L_%(2)s_seg.nii.gz' % {"1" : j, "2" : i}), op_string=('-thr %(1)s -uthr %(2)s' % {"1" : j, "2" : j})).run()
# binarize
ImageMaths(in_file=('%(1)s_L_%(2)s_seg.nii.gz' % {"1" : j, "2" : i}), out_file=('%(1)s_L_%(2)s_seg.nii.gz' % {"1" : j, "2" : i}), op_string=("-bin")).run()
# now calc average DICE per segement per Subject
for i in sublist:
for j in seglist:
# get volume A
stats = ImageStats(in_file=('%(1)s_L_%(2)s_seg.nii.gz' % {"1" : j, "2" : i}), op_string='-V').run()
volume_A = stats.outputs.out_stat[1]
# get for intersection for one area each other subject
# first make sublist of participants not including self
sect_list = filter (lambda a: a != i, sublist)
Dice_list= [0]*(len(sect_list))
def get_wf_tissue_masks(name='wf_tissue_masks'):
'''
This Function gives a workflow that resamples the T1 brains, extracts the
tissue types thresholds at 0.5 and registers them to T2* space
It then registers the tissue priors to the T2* space and then performs a
bitwise AND between two maps.
'''
# csf_tissue_prior_path, gm_tissue_prior_path, wm_tissue_prior_path,
# threshold = 0.5
wf_tissue_masks = Workflow(name=name)
inputspec = Node(IdentityInterface(fields=[
'resampled_anat_file_path', 'func2anat_mat_path', 'std2func_mat_path',
'reference_func_file_path', 'brain_mask_eroded', 'threshold'
]),
name="inputspec")
# FSL FAST node to segment the T1 brain
fast = Node(FAST(out_basename='fast_'), name='fast')
# probability_maps=True,segments=True,
wf_tissue_masks.connect(inputspec, 'resampled_anat_file_path', fast,
'in_files')
# Invert the func2anat matrix to get anat2func
inv_mat = Node(ConvertXFM(invert_xfm=True), name='inv_mat')
wf_tissue_masks.connect(inputspec, 'func2anat_mat_path', inv_mat,
'in_file')
# Transform the above segmented tissue masks to the functional space using the inverse matrix
anat2func_xform_csf = Node(FLIRT(output_type='NIFTI',
apply_xfm=True,
interp='sinc'),
name='anat2func_xform_csf')
wf_tissue_masks.connect(inputspec, 'reference_func_file_path',
anat2func_xform_csf, 'reference')
wf_tissue_masks.connect(inv_mat, 'out_file', anat2func_xform_csf,
'in_matrix_file')
anat2func_xform_wm = Node(FLIRT(output_type='NIFTI',
apply_xfm=True,
interp='sinc'),
name='anat2func_xform_wm')
wf_tissue_masks.connect(inputspec, 'reference_func_file_path',
anat2func_xform_wm, 'reference')
wf_tissue_masks.connect(inv_mat, 'out_file', anat2func_xform_wm,
'in_matrix_file')
std2func_xform_eroded_brain = Node(FLIRT(output_type='NIFTI',
apply_xfm=True,
interp='nearestneighbour'),
name='std2func_xform_eroded_brain')
wf_tissue_masks.connect(inputspec, 'reference_func_file_path',
std2func_xform_eroded_brain, 'reference')
wf_tissue_masks.connect(inputspec, 'std2func_mat_path',
std2func_xform_eroded_brain, 'in_matrix_file')
def select_item_from_array(arr, index=0):
import numpy as np
arr = np.array(arr)
return arr[index]
wf_tissue_masks.connect(
fast, ('partial_volume_files', select_item_from_array, 0),
anat2func_xform_csf, 'in_file')
wf_tissue_masks.connect(
fast, ('partial_volume_files', select_item_from_array, 2),
anat2func_xform_wm, 'in_file')
wf_tissue_masks.connect(inputspec, 'brain_mask_eroded',
std2func_xform_eroded_brain, 'in_file')
# Threshold
def get_opstring(threshold):
op = '-thr ' + str(threshold) + ' -bin'
return op
# print(inputspec.outputs)
# ----- CSF ------
threshold_csf = Node(interface=ImageMaths(suffix='_thresh'),
name='threshold_csf')
# threshold_csf.inputs.op_string = '-thresh '+str(inputspec.outputs.threshold)+' -bin'
wf_tissue_masks.connect(inputspec, ('threshold', get_opstring),
threshold_csf, 'op_string')
wf_tissue_masks.connect(anat2func_xform_csf, 'out_file', threshold_csf,
'in_file')
# ------- GM --------
# threshold_gm = Node(interface=ImageMaths(op_string='-thresh',
# suffix='_thresh'),
# name='threshold_gm')
#
#
# wf_tissue_priors.connect(inputspec, ('threshold', get_opstring), threshold_gm, 'op_string' )
# wf_tissue_priors.connect(fast, partial_volume_map[1], threshold_gm, 'in_file')
#
# -------- WM --------
threshold_wm = Node(interface=ImageMaths(suffix='_thresh'),
name='threshold_wm')
wf_tissue_masks.connect(inputspec, ('threshold', get_opstring),
threshold_wm, 'op_string')
wf_tissue_masks.connect(anat2func_xform_wm, 'out_file', threshold_wm,
'in_file')
# -------------------
#
# wf_tissue_masks.connect(threshold_csf, 'out_file', std2func_xform_csf, 'in_file')
# wf_tissue_masks.connect(threshold_wm, 'out_file', std2func_xform_wm, 'in_file')
# Masking the outer brain CSF
csf_mask = Node(interface=ApplyMask(), name='csf_mask')
wf_tissue_masks.connect(threshold_csf, 'out_file', csf_mask, 'in_file')
wf_tissue_masks.connect(std2func_xform_eroded_brain, 'out_file', csf_mask,
'mask_file')
# Masking the outer brain WM that might be present due to poor BET
wm_mask = Node(interface=ApplyMask(), name='wm_mask')
wf_tissue_masks.connect(threshold_wm, 'out_file', wm_mask, 'in_file')
wf_tissue_masks.connect(std2func_xform_eroded_brain, 'out_file', wm_mask,
'mask_file')
# wm_mask = Node(interface=ApplyMask(),
# name='wm_mask')
# wf_tissue_masks.connect(std2func_xform_wm, 'out_file', wm_mask, 'in_file')
# wf_tissue_masks.connect(std2func_xform_wm_prior, 'out_file', wm_mask, 'mask_file')
outputspec = Node(IdentityInterface(fields=['csf_mask', 'wm_mask']),
name="outputspec")
wf_tissue_masks.connect(csf_mask, 'out_file', outputspec, 'csf_mask')
# wf_tissue_priors.connect(threshold_gm, 'out_file', outputspec, 'gm_tissue_prior_path')
wf_tissue_masks.connect(wm_mask, 'out_file', outputspec, 'wm_mask')
return wf_tissue_masks
def init_hcp_segment_anat_wf(name='hcp_segment_anat_wf'):
"""
This workflow generates WM, CSF and GM masks using the same
pipeline from the HCP pipeline. The wm and csf masks are created by
importing the appropriate freesurfer parcellations from the wmparc
file and subtracting out the voxel marked as gm.
**Paramters**
name
Name for the workflow hierarchy of Niype
**Inputs**
brainmask_fs
freesurfer brain in MNI space with anat dims
l_atlasroi
left vertex mask
l_midthickness
left midthickness surface
l_white
left white matter surface
l_pial
left pial surface
r_atlasroi
right vertex mask
r_midthickness
right midthickness surface
r_white
right white matter surface
r_pial
right pial surface
wmparc
gyral white matter segmentation generated by freesurfer warped
MNI space
ROIs
subcortical parcellation of brain warped into MNI space
**Outputs**
brain_gm_mask
whole brain gm mask dilated twice in MNI 2mm space brainmasked
cortical_gm_mask
coritcal gm mask in MNI 2mm space brainmasked
subcortical_gm_mask
subcortical gm mask in MNI 2mm space brainmasked
wm_mask
white matter mask in MNI 2mm space brainmasked
csf_mask
csf mask in MNI 2mm space brainmasked
"""
wf = Workflow(name='hcp_segment')
with pkg_resources.path(data, 'FreeSurferCSFRegLut.txt') as tmp:
csf_rois = str(tmp)
with pkg_resources.path(data, 'FreeSurferWMRegLut.txt') as tmp:
wm_rois = str(tmp)
with pkg_resources.path(data, 'fsl_identity.mat') as tmp:
fsl_identity = str(tmp)
inputnode = Node(IdentityInterface(
fields=['brainmask_fs', 'wmparc', 'l_atlasroi', 'l_midthickness', 'l_white',
'l_pial', 'r_atlasroi', 'r_midthickness', 'r_white', 'r_pial',
'ROIs']),
name='inputnode')
outputnode = Node(IdentityInterface(
fields=['cort_gm_mask', 'subcort_gm_mask', 'gm_mask',
'wm_mask', 'csf_mask']),
name='outputnode')
# resample gm mask to 2mm MNI space
resample_mask = Node(ApplyWarp(relwarp=True, interp='nn',
premat=fsl_identity, out_file='brainmask_fs.2.nii.gz'),
name='resample_mask')
# gm mask nodes
l_gm_mask = Node(wb.MetricToVolumeMappingRC(out_file='l_gm_mask.nii.gz'),
name='l_gm_mask')
r_gm_mask = Node(wb.MetricToVolumeMappingRC(out_file='r_gm_mask.nii.gz'),
name='r_gm_mask')
cort_gm = Node(ImageMaths(out_file='cortical_gm.nii.gz',
op_string='-add',
args='-bin'),
name='cort_gm')
cort_gm_mask = Node(ImageMaths(out_file='cortical_gm_mask.nii.gz',
op_string='-mul'),
name='cort_gm_mask')
subcort_gm_mask = Node(ImageMaths(out_file='subcortical_gm_mask.nii.gz',
op_string='-mul',
args='-bin'),
name='subcort_gm_mask')
brain_gm_mask = Node(ImageMaths(out_file='brain_gm_mask.nii.gz',
op_string='-add',
args='-dilD -dilD'),
name='brain_gm_mask')
# wm mask nodes
wm_vol = Node(wb.VolumeLabelImport(out_file='wm_vol.nii.gz',
label_list_file=wm_rois,
discard_others=True,
drop_unused_labels=True),
name='wm_vol')
wm = Node(ImageMaths(out_file='wm.nii.gz',
op_string='-bin -sub',
args='-bin'),
name='wm')
wm_mask = Node(ImageMaths(out_file='wm_mask.nii.gz',
op_string='-mul',
args='-bin'),
name='wm_mask')
# csf mask nodes
csf_vol = Node(wb.VolumeLabelImport(out_file='csf_vol.nii.gz',
label_list_file=csf_rois,
discard_others=True,
drop_unused_labels=True),
name='csf_vol')
csf = Node(ImageMaths(out_file='csf.nii.gz',
op_string='-bin -sub',
args='-bin'),
name='csf')
csf_mask = Node(ImageMaths(out_file='csf_mask.nii.gz',
op_string='-mul',
args='-bin'),
name='csf_mask')
wf.connect([
# gm
(inputnode, resample_mask, [('brainmask_fs', 'in_file'),
('wmparc', 'ref_file')]),
(inputnode, l_gm_mask, [('l_atlasroi', 'in_file'),
('l_midthickness', 'surface'),
('wmparc', 'volume_space'),
('l_pial', 'inner_surf'),
('l_white', 'outer_surf')]),
(inputnode, r_gm_mask, [('r_atlasroi', 'in_file'),
('r_midthickness', 'surface'),
('wmparc', 'volume_space'),
('r_pial', 'inner_surf'),
('r_white', 'outer_surf')]),
(l_gm_mask, cort_gm, [('out_file', 'in_file')]),
(r_gm_mask, cort_gm, [('out_file', 'in_file2')]),
(cort_gm, cort_gm_mask, [('out_file', 'in_file')]),
(resample_mask, cort_gm_mask, [('out_file', 'in_file2')]),
(inputnode, subcort_gm_mask, [('ROIs', 'in_file')]),
(resample_mask, subcort_gm_mask, [('out_file', 'in_file2')]),
(cort_gm_mask, brain_gm_mask, [('out_file', 'in_file')]),
(subcort_gm_mask, brain_gm_mask, [('out_file', 'in_file2')]),
# wm
(inputnode, wm_vol, [('wmparc', 'in_file')]),
(wm_vol, wm, [('out_file', 'in_file')]),
(brain_gm_mask, wm, [('out_file', 'in_file2')]),
(wm, wm_mask, [('out_file', 'in_file')]),
(resample_mask, wm_mask, [('out_file', 'in_file2')]),
# csf
(inputnode, csf_vol, [('wmparc', 'in_file')]),
(csf_vol, csf, [('out_file', 'in_file')]),
(brain_gm_mask, csf, [('out_file', 'in_file2')]),
(csf, csf_mask, [('out_file', 'in_file')]),
(resample_mask, csf_mask, [('out_file', 'in_file2')]),
# output
(cort_gm_mask, outputnode, [('out_file', 'cort_gm_mask')]),
(subcort_gm_mask, outputnode, [('out_file', 'subcort_gm_mask')]),
(brain_gm_mask, outputnode, [('out_file', 'brain_gm_mask')]),
(wm_mask, outputnode, [('out_file', 'wm_mask')]),
(csf_mask, outputnode, [('out_file', 'csf_mask')])
])
return wf
def functional_per_participant_test():
for i in ["","_aF","_cF1","_cF2","_pF"]:
template = "~/ni_data/templates/ds_QBI_chr.nii.gz"
participant = "4008"
image_dir = "~/ni_data/ofM.dr/preprocessing/generic_work/_subject_session_{}.ofM{}/_scan_type_7_EPI_CBV/temporal_mean/".format(participant,i)
try:
for myfile in os.listdir(image_dir):
if myfile.endswith(".nii.gz"):
mimage = os.path.join(image_dir,myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = mimage
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200,200,200,200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = 'n4_{}_ofM{}.nii.gz'.format(participant,i)
n4_res = n4.run()
functional_cutoff = ImageMaths()
functional_cutoff.inputs.op_string = "-thrP 30"
functional_cutoff.inputs.in_file = n4_res.outputs.output_image
functional_cutoff_res = functional_cutoff.run()
functional_BET = BET()
functional_BET.inputs.mask = True
functional_BET.inputs.frac = 0.5
functional_BET.inputs.in_file = functional_cutoff_res.outputs.out_file
functional_BET_res = functional_BET.run()
registration = ants.Registration()
registration.inputs.fixed_image = template
registration.inputs.output_transform_prefix = "output_"
registration.inputs.transforms = ['Affine', 'SyN']
registration.inputs.transform_parameters = [(0.1,), (3.0, 3.0, 5.0)]
registration.inputs.number_of_iterations = [[10000, 10000, 10000], [100, 100, 100]]
registration.inputs.dimension = 3
registration.inputs.write_composite_transform = True
registration.inputs.collapse_output_transforms = True
registration.inputs.initial_moving_transform_com = True
registration.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
registration.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
registration.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
registration.inputs.sampling_strategy = ['Regular'] * 2 + [[None, None]]
registration.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
registration.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
registration.inputs.convergence_window_size = [20] * 2 + [5]
registration.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
registration.inputs.sigma_units = ['vox'] * 3
registration.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]]
registration.inputs.use_estimate_learning_rate_once = [True] * 3
registration.inputs.use_histogram_matching = [False] * 2 + [True]
registration.inputs.winsorize_lower_quantile = 0.005
registration.inputs.winsorize_upper_quantile = 0.995
registration.inputs.args = '--float'
registration.inputs.num_threads = 4
registration.plugin_args = {'qsub_args': '-pe orte 4', 'sbatch_args': '--mem=6G -c 4'}
registration.inputs.moving_image = functional_BET_res.outputs.out_file
registration.inputs.output_warped_image = '{}_ofM{}.nii.gz'.format(participant,i)
res = registration.run()