def calculate_realignment_cost(target_id: str,
cost_function: str,
serialize: bool = True):
realigned_subject_dirs = generate_subject_dirs("realigned", target_id,
cost_function)
target_scan = get_target_scan(target_id)
costs = {}
for subject_dir in realigned_subject_dirs:
subject_id = subject_dir.split("/")[-2]
registered, mat_file = get_realigned_subject_data(subject_id)
print(f"Calculating cost function value...", end="\t")
flirt = FLIRT()
flirt.inputs.in_file = registered
flirt.inputs.reference = target_scan
flirt.inputs.schedule = "/usr/local/fsl/etc/flirtsch/measurecost1.sch"
flirt.inputs.in_matrix_file = mat_file
tmp = os.path.join(subject_dir, "tmp")
flirt.inputs.out_file = os.path.join(tmp, "cost.nii.gz")
flirt.inputs.out_matrix_file = os.path.join(tmp, "cost.mat")
os.makedirs(tmp, exist_ok=True)
f = flirt.run()
result = float(f.runtime.stdout.split()[0])
print(f"done! [{result}]")
shutil.rmtree(tmp)
costs[subject_id] = result
if serialize:
serialize_results(target_id, cost_function, costs)
return costs
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 flirt_t1_epi(subject_id, data_dir, run, sink_dir):
def get_niftis(subject_id, data_dir, run, sink_dir):
from os.path import join, exists
t1 = join(
data_dir,
subject_id,
"session-1",
"anatomical",
"anatomical-0",
"anatomical.nii.gz",
)
# t1_brain_mask = join(data_dir, subject, 'session-1', 'anatomical', 'anatomical-0', 'fsl', 'anatomical-bet.nii.gz')
ex_func = join(
sink_dir,
subject_id,
"{0}-{1}_retr-example_func.nii.gz".format(subject_id, run),
)
assert exists(t1), "t1 does not exist"
assert exists(ex_func), "example func does not exist"
standard = "/home/applications/fsl/5.0.8/data/standard/MNI152_T1_2mm.nii.gz"
return t1, ex_func, standard
coreg = join(sink_dir, "qa", "{0}-{1}_t1_flirt.png".format(subject, run))
data = Function(
function=get_niftis,
input_names=["subject_id", "data_dir", "run", "sink_dir"],
output_names=["t1", "ex_func", "standard"],
)
data.inputs.data_dir = data_dir
data.inputs.sink_dir = sink_dir
data.inputs.subject_id = subject
data.inputs.run = run
grabber = data.run()
re_flit = FLIRT(
cost_func="normmi",
dof=12,
searchr_x=[-90, 90],
searchr_y=[-90, 90],
searchr_z=[-90, 90],
interp="trilinear",
bins=256,
)
re_flit.inputs.reference = grabber.outputs.ex_func
re_flit.inputs.in_file = grabber.outputs.t1
re_flit.inputs.out_file = join(
sink_dir, subject, "{0}-{1}_t1-flirt-retr.nii.gz".format(subject, run))
re_flit.inputs.out_matrix_file = join(
sink_dir, subject, "{0}-{1}_t1-flirt-retr.mat".format(subject, run))
reg_func = re_flit.run()
display = plotting.plot_anat(grabber.outputs.ex_func, dim=0)
display.add_edges(reg_func.outputs.out_file)
display.savefig(coreg, dpi=300)
return
def mask_CTBrain(CT_dir, T1_dir, frac):
# nav to dir with T1 images
os.chdir(T1_dir)
# run BET to extract brain from T1
bet = BET()
bet.inputs.in_file = T1_dir + '/T1.nii'
bet.inputs.frac = frac
bet.inputs.robust = True
bet.inputs.mask = True
print "::: Extracting Brain mask from T1 using BET :::"
bet.run()
# use flrit to correg CT to T1
flirt = FLIRT()
flirt.inputs.in_file = CT_dir + '/CT.nii'
flirt.inputs.reference = T1_dir + '/T1.nii'
flirt.inputs.cost_func = 'mutualinfo'
print "::: Estimating corregistration from CT to T1 using FLIRT :::"
flirt.run()
# get inverse of estimated coreg of CT tp T1
print "::: Estimating inverse affine for Brain mask of CT :::"
os.system('convert_xfm -omat inv_CT_flirt.mat -inverse CT_flirt.mat')
os.system('mv inv_CT_flirt.mat %s' % (CT_dir))
# apply inverse affine coreg to get brain mask in CT space
applyxfm = ApplyXfm()
applyxfm.inputs.in_file = T1_dir + '/T1_brain_mask.nii.gz'
applyxfm.inputs.in_matrix_file = CT_dir + '/inv_CT_flirt.mat'
applyxfm.inputs.out_file = CT_dir + '/CT_mask.nii.gz'
applyxfm.inputs.reference = CT_dir + '/CT.nii'
applyxfm.inputs.apply_xfm = True
print "::: Applying inverse affine to Brain mask to get CT mask :::"
applyxfm.run()
# dilate brain mask to make sure all elecs are in final masked img
CT_mask = nib.load(CT_dir + '/CT_mask.nii.gz')
CT_mask_dat = CT_mask.get_data()
kernel = np.ones((5, 5), np.uint8)
print "::: Dilating CT mask :::"
dilated = cv2.dilate(CT_mask_dat, kernel, iterations=1)
hdr = CT_mask.get_header()
affine = CT_mask.get_affine()
N = nib.Nifti1Image(dilated, affine, hdr)
new_fname = CT_dir + '/dilated_CT_mask.nii'
N.to_filename(new_fname)
# apply mask to CT
os.chdir(CT_dir)
print "::: masking CT with dilated brain mask :::"
os.system(
"fslmaths 'CT.nii' -mas 'dilated_CT_mask.nii.gz' 'masked_CT.nii'")
os.system('gunzip masked_CT.nii.gz')
def create_workflow_coreg_epi2t1w():
input_node = Node(IdentityInterface(fields=[
'bold_mean',
't2star_fov',
't2star_whole',
't1w',
]), name='input')
output = Node(IdentityInterface(fields=[
'mat_epi2t1w',
]), name='output')
# node skull
skull = Node(interface=BET(), name="skull_stripping")
coreg_epi2fov = Node(FLIRT(), name='epi_2_fov')
coreg_epi2fov.inputs.cost = 'mutualinfo'
coreg_epi2fov.inputs.dof = 12
coreg_epi2fov.inputs.no_search = True
coreg_epi2fov.inputs.output_type = 'NIFTI_GZ'
coreg_fov2whole = Node(FLIRT(), name='fov_2_whole')
coreg_fov2whole.inputs.cost = 'mutualinfo'
coreg_fov2whole.inputs.dof = 6
coreg_fov2whole.inputs.output_type = 'NIFTI_GZ'
coreg_whole2t1w = Node(EpiReg(), name='whole_2_t1w')
concat_fov2t1w = Node(interface=ConvertXFM(), name='mat_fov2t1w')
concat_fov2t1w.inputs.concat_xfm = True
concat_epi2t1w = Node(interface=ConvertXFM(), name='mat_epi2t1w')
concat_epi2t1w.inputs.concat_xfm = True
w = Workflow('coreg_epi2t1w')
w.connect(input_node, 'bold_mean', coreg_epi2fov, 'in_file')
w.connect(input_node, 't2star_fov', coreg_epi2fov, 'reference')
w.connect(input_node, 't2star_fov', coreg_fov2whole, 'in_file')
w.connect(input_node, 't2star_whole', coreg_fov2whole, 'reference')
w.connect(input_node, 't1w', skull, 'in_file')
w.connect(input_node, 't2star_whole', coreg_whole2t1w, 'epi')
w.connect(skull, 'out_file', coreg_whole2t1w, 't1_brain')
w.connect(input_node, 't1w', coreg_whole2t1w, 't1_head')
w.connect(coreg_fov2whole, 'out_matrix_file', concat_fov2t1w, 'in_file')
w.connect(coreg_whole2t1w, 'epi2str_mat', concat_fov2t1w, 'in_file2')
w.connect(coreg_epi2fov, 'out_matrix_file', concat_epi2t1w, 'in_file')
w.connect(concat_fov2t1w, 'out_file', concat_epi2t1w, 'in_file2')
w.connect(concat_epi2t1w, 'out_file', output, 'mat_epi2t1w')
return w
def func_register(img_original,img_template, img_registered):
# img_original : original T2 or FLAIR image file
# img_template : isovoxel T1C file used for registration template
# img_registered :file name that stores registered (isovoxel) T2 or FLAIR file
coregi_iso = FLIRT(bins=640, cost_func='mutualinfo', dof=12, output_type="NIFTI_GZ", verbose=0,
datatype = 'float', interp = 'trilinear',
in_file = img_original,
reference = img_template,
out_file = img_registered)
coregi_iso.run()
def mask_CTBrain(CT_dir, T1_dir, frac):
# nav to dir with T1 images
os.chdir(T1_dir)
# run BET to extract brain from T1
bet = BET()
bet.inputs.in_file = T1_dir + "/T1.nii"
bet.inputs.frac = frac
bet.inputs.robust = True
bet.inputs.mask = True
print "::: Extracting Brain mask from T1 using BET :::"
bet.run()
# use flrit to correg CT to T1
flirt = FLIRT()
flirt.inputs.in_file = CT_dir + "/CT.nii"
flirt.inputs.reference = T1_dir + "/T1.nii"
flirt.inputs.cost_func = "mutualinfo"
print "::: Estimating corregistration from CT to T1 using FLIRT :::"
flirt.run()
# get inverse of estimated coreg of CT tp T1
print "::: Estimating inverse affine for Brain mask of CT :::"
os.system("convert_xfm -omat inv_CT_flirt.mat -inverse CT_flirt.mat")
os.system("mv inv_CT_flirt.mat %s" % (CT_dir))
# apply inverse affine coreg to get brain mask in CT space
applyxfm = ApplyXfm()
applyxfm.inputs.in_file = T1_dir + "/T1_brain_mask.nii.gz"
applyxfm.inputs.in_matrix_file = CT_dir + "/inv_CT_flirt.mat"
applyxfm.inputs.out_file = CT_dir + "/CT_mask.nii.gz"
applyxfm.inputs.reference = CT_dir + "/CT.nii"
applyxfm.inputs.apply_xfm = True
print "::: Applying inverse affine to Brain mask to get CT mask :::"
applyxfm.run()
# dilate brain mask to make sure all elecs are in final masked img
CT_mask = nib.load(CT_dir + "/CT_mask.nii.gz")
CT_mask_dat = CT_mask.get_data()
kernel = np.ones((5, 5), np.uint8)
print "::: Dilating CT mask :::"
dilated = cv2.dilate(CT_mask_dat, kernel, iterations=1)
hdr = CT_mask.get_header()
affine = CT_mask.get_affine()
N = nib.Nifti1Image(dilated, affine, hdr)
new_fname = CT_dir + "/dilated_CT_mask.nii"
N.to_filename(new_fname)
# apply mask to CT
os.chdir(CT_dir)
print "::: masking CT with dilated brain mask :::"
os.system("fslmaths 'CT.nii' -mas 'dilated_CT_mask.nii.gz' 'masked_CT.nii'")
os.system("gunzip masked_CT.nii.gz")
def isotropic_voxels():
if verbose:
print('Resampling to isotropic voxels')
orig = nib.load('%s/opposedphase.nii.gz' % tmpdir)
for f in ['opposedphase', 'inphase']:
iso = FLIRT()
iso.inputs.in_file = '%s/%s.nii.gz' % (tmpdir, f)
iso.inputs.reference = '%s/%s.nii.gz' % (tmpdir, f)
iso.inputs.out_file = '%s/%s_iso.nii.gz' % (tmpdir, f)
iso.inputs.apply_isoxfm = orig.header.get_zooms()[0]
iso.run()
def make_w_coreg_7T_3T(ttype=''):
n_in = Node(IdentityInterface(fields=[
'T1w_7T',
'T1w_3T',
]), name='input')
n_out = Node(IdentityInterface(fields=[
'mat_t1w3t_to_t1w7t',
'mat_t1w7t_to_t1w3t',
]),
name='output')
n_7T = Node(Reorient2Std(), '7T')
n_3T = Node(Reorient2Std(), '3T')
n_coarse = Node(FLIRT(), 'coarse')
n_coarse.inputs.no_search = True
n_coarse.inputs.schedule = environ[
'FSLDIR'] + '/etc/flirtsch/sch3Dtrans_3dof'
n_coarse.inputs.dof = 6
n_fine = Node(FLIRT(), 'fine')
n_fine.inputs.no_search = True
# n_fine.inputs.cost = 'normcorr'
n_fine.inputs.dof = 7
n_3t_7t = Node(ConvertXFM(), name='t1w3t_to_t1w7t')
n_3t_7t.inputs.concat_xfm = True
n_3t_7t.inputs.out_file = 'mat_t1w3t_to_t1w7t.mat'
n_7t_3t = Node(ConvertXFM(), name='t1w7t_to_t1w3t')
n_7t_3t.inputs.invert_xfm = True
n_7t_3t.inputs.out_file = 'mat_t1w7t_to_t1w3t.mat'
w = Workflow('coreg_3T_7T' + ttype)
w.connect(n_in, 'T1w_7T', n_7T, 'in_file')
w.connect(n_in, 'T1w_3T', n_3T, 'in_file')
w.connect(n_7T, 'out_file', n_coarse, 'reference')
w.connect(n_3T, 'out_file', n_coarse, 'in_file')
w.connect(n_7T, 'out_file', n_fine, 'reference')
w.connect(n_coarse, 'out_file', n_fine, 'in_file')
w.connect(n_coarse, 'out_matrix_file', n_3t_7t, 'in_file')
w.connect(n_fine, 'out_matrix_file', n_3t_7t, 'in_file2')
w.connect(n_3t_7t, 'out_file', n_7t_3t, 'in_file')
w.connect(n_3t_7t, 'out_file', n_out, 'mat_t1w3t_to_t1w7t')
w.connect(n_7t_3t, 'out_file', n_out, 'mat_t1w7t_to_t1w3t')
return w
def _flirt_linear_coreg_pipeline(self, **name_maps):
"""
Registers a MR scan to a refernce MR scan using FSL's FLIRT command
"""
pipeline = self.new_pipeline(
name='linear_coreg',
name_maps=name_maps,
desc="Registers a MR scan against a reference image using FLIRT",
citations=[fsl_cite])
pipeline.add(
'flirt',
FLIRT(dof=self.parameter('flirt_degrees_of_freedom'),
cost=self.parameter('flirt_cost_func'),
cost_func=self.parameter('flirt_cost_func'),
output_type='NIFTI_GZ'),
inputs={
'in_file': ('mag_preproc', nifti_gz_format),
'reference': ('coreg_ref', nifti_gz_format)},
outputs={
'mag_coreg': ('out_file', nifti_gz_format),
'coreg_fsl_mat': ('out_matrix_file', text_matrix_format)},
requirements=[fsl_req.v('5.0.8')],
wall_time=5)
return pipeline
def _qform_transform_factory(self, name, to_reg, ref, qformed, qformed_mat,
**kwargs):
pipeline = self.create_pipeline(
name=name,
inputs=[
DatasetSpec(to_reg, nifti_gz_format),
DatasetSpec(ref, nifti_gz_format)
],
outputs=[
DatasetSpec(qformed, nifti_gz_format),
DatasetSpec(qformed_mat, text_matrix_format)
],
desc="Registers a MR scan against a reference image",
version=1,
citations=[fsl_cite],
**kwargs)
flirt = pipeline.create_node(interface=FLIRT(),
name='flirt',
requirements=[fsl5_req],
wall_time=5)
flirt.inputs.uses_qform = True
flirt.inputs.apply_xfm = True
# Connect inputs
pipeline.connect_input(to_reg, flirt, 'in_file')
pipeline.connect_input(ref, flirt, 'reference')
# Connect outputs
pipeline.connect_output(qformed, flirt, 'out_file')
pipeline.connect_output(qformed_mat, flirt, 'out_matrix_file')
return pipeline
def create_workflow_hrfpattern_7T(glm='spm'):
input_node = Node(IdentityInterface(fields=[
'bold',
'events',
't2star_fov',
't2star_whole',
't1w',
]),
name='input')
coreg_tstat = Node(interface=FLIRT(), name='realign_result_to_anat')
coreg_tstat.inputs.apply_xfm = True
w = Workflow('hrf_7T')
w_preproc = create_workflow_preproc_spm()
if glm == 'spm':
w_hrfpattern = create_workflow_hrfpattern_spm()
elif glm == 'fsl':
w_hrfpattern = create_workflow_hrfpattern_fsl()
w_coreg = create_workflow_coreg_epi2t1w()
w.connect(input_node, 'bold', w_preproc, 'input.bold')
w.connect(input_node, 'events', w_hrfpattern, 'input.events')
w.connect(input_node, 't2star_fov', w_coreg, 'input.t2star_fov')
w.connect(input_node, 't2star_whole', w_coreg, 'input.t2star_whole')
w.connect(input_node, 't1w', w_coreg, 'input.t1w')
w.connect(input_node, 't1w', coreg_tstat, 'reference')
w.connect(w_preproc, 'realign.realigned_files', w_hrfpattern, 'input.bold')
w.connect(w_preproc, 'realign.mean_image', w_coreg, 'input.bold_mean')
w.connect(w_hrfpattern, 'output.T_image', coreg_tstat, 'in_file')
w.connect(w_coreg, 'output.mat_epi2t1w', coreg_tstat, 'in_matrix_file')
return w
def qform_transform_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='qform_transform',
name_maps=name_maps,
desc="Registers a MR scan against a reference image",
citations=[fsl_cite])
if self.provided('coreg_ref'):
in_file = 'mag_preproc'
reference = 'coreg_ref'
elif self.provided('coreg_ref_brain'):
in_file = 'brain'
reference = 'coreg_ref_brain'
else:
raise BananaUsageError(
"'coreg_ref' or 'coreg_ref_brain' need to be provided to "
"study in order to run qform_transform")
pipeline.add(
'flirt',
FLIRT(
uses_qform=True,
apply_xfm=True,
output_type='NIFTI_GZ'),
inputs={
'in_file': (in_file, nifti_gz_format),
'reference': (reference, nifti_gz_format)},
outputs={
'qformed': ('out_file', nifti_gz_format),
'qform_mat': ('out_matrix_file', text_matrix_format)},
requirements=[fsl_req.v('5.0.8')],
wall_time=5)
return pipeline
def register_T1_to_simnibs(self):
### run flirt registartion if it has not been run before
dest_img = os.path.join(self.mesh_dir, 'm2m_' + self.subject,
'T1fs_conform.nii.gz')
if not os.path.exists(
os.path.join(self.wf_base_dir, 'T1_to_simnibs_registration')):
flirt = Node(FLIRT(), name='flirt')
flirt.inputs.in_file = os.path.join(self.mesh_dir,
'm2m_' + self.subject,
'T1fs.nii.gz')
flirt.inputs.reference = dest_img
flirt.inputs.out_file = 'T1_in_Simnibs.nii.gz'
flirt.inputs.out_matrix_file = 'T12Simnibs.mat'
flirt.inputs.searchr_x = [-180, 180]
flirt.inputs.searchr_y = [-180, 180]
flirt.inputs.searchr_z = [-180, 180]
wf = Workflow(name='T1_to_simnibs_registration',
base_dir=self.wf_base_dir)
wf.add_nodes([flirt])
wf.run()
## path to registration file
t12simnibs_reg = os.path.join(self.wf_base_dir,
'T1_to_simnibs_registration', 'flirt',
'T12Simnibs.mat')
return t12simnibs_reg
def run_t2w_deface(image, t1w_deface_mask, outfile):
"""
Setup and run t2w defacing workflow.
Parameters
----------
image : str
Path to image that should be defaced.
t1w_deface_mask : str
Path to the defaced T1w image that will be used
as defacing mask.
outfile : str
Name of the defaced file.
"""
from bidsonym.utils import deface_t2w
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']),
name='inputnode')
flirtnode = pe.Node(FLIRT(cost_func='mutualinfo',
output_type="NIFTI_GZ"),
name='flirtnode')
deface_t2w = pe.Node(Function(input_names=['image', 'warped_mask', 'outfile'],
output_names=['outfile'],
function=deface_t2w),
name='deface_t2w')
deface_wf.connect([(inputnode, flirtnode, [('in_file', 'reference')]),
(inputnode, deface_t2w, [('in_file', 'image')]),
(flirtnode, deface_t2w, [('out_file', 'warped_mask')])])
inputnode.inputs.in_file = image
flirtnode.inputs.in_file = t1w_deface_mask
deface_t2w.inputs.outfile = outfile
deface_wf.run()
def create_workflow_temporalpatterns_7T(subjects, runs):
input_node = Node(IdentityInterface(fields=[
'bold',
'events',
't2star_fov',
't2star_whole',
't1w',
]), name='input')
coreg_tstat = MapNode(
interface=FLIRT(), name='realign_result_to_anat',
iterfield=['in_file', ])
coreg_tstat.inputs.apply_xfm = True
w = Workflow('temporalpatterns_7T')
w_preproc = create_workflow_preproc_spm()
w_spatialobject = create_workflow_temporalpatterns_fsl()
w_coreg = create_workflow_coreg_epi2t1w()
w.connect(input_node, 'bold', w_preproc, 'input.bold')
w.connect(input_node, 'events', w_spatialobject, 'input.events')
w.connect(input_node, 't2star_fov', w_coreg, 'input.t2star_fov')
w.connect(input_node, 't2star_whole', w_coreg, 'input.t2star_whole')
w.connect(input_node, 't1w', w_coreg, 'input.t1w')
w.connect(input_node, 't1w', coreg_tstat, 'reference')
w.connect(w_preproc, 'realign.realigned_files', w_spatialobject, 'input.bold')
w.connect(w_preproc, 'realign.mean_image', w_coreg, 'input.bold_mean')
w.connect(w_spatialobject, 'output.T_image', coreg_tstat, 'in_file')
w.connect(w_coreg, 'output.mat_epi2t1w', coreg_tstat, 'in_matrix_file')
return w
def func_regi2mni(path_T1C_isovoxel, path_mask_isovoxel):
matrix_2mni = 'matrix_2mni.mat'
mni_reference = 'MNI152_T1_1mm_brain.nii.gz'
coregi_t1gd2mni= FLIRT(bins=640, cost_func='mutualinfo', dof=12, output_type="NIFTI_GZ", verbose=0,
datatype = 'float', interp = 'trilinear',
in_file = path_T1C_isovoxel,
reference = mni_reference,
out_file = 'img_2mni.nii.gz',
out_matrix_file = matrix_2mni)
coregi_t1gd2mni.run()
coregi_mask2MNI = ApplyXFM(in_file = path_mask_isovoxel,
in_matrix_file = matrix_2mni,
out_file = 'mask_2mni.nii.gz',
reference= mni_reference)
coregi_mask2MNI.run()
def resample_to_umap(DeepX, reference):
if verbose:
print('Resampling to umap resolution')
# Rehape to in-phase resolution
DeepX = np.swapaxes(np.flipud(np.fliplr(DeepX)), 2, 0)
DeepX_padded = np.zeros(reference.shape)
DeepX_padded[96:288, 6:198, :192] = DeepX
DeepX_nii = nib.Nifti1Image(DeepX_padded, reference.affine,
reference.header)
nib.save(DeepX_nii, '%s/DeepDixon.nii.gz' % tmpdir)
# Resample to UMAP resolution
DeepX_rsl = FLIRT()
DeepX_rsl.inputs.in_file = '%s/DeepDixon.nii.gz' % tmpdir
DeepX_rsl.inputs.reference = '%s/umap.nii.gz' % tmpdir
DeepX_rsl.inputs.out_file = '%s/DeepDixon_rsl.nii.gz' % tmpdir
DeepX_rsl.run()
DeepX = nib.load('%s/DeepDixon_rsl.nii.gz' % tmpdir).get_fdata()
DeepX = DeepX.astype(np.uint16)
DeepX = np.fliplr(np.flipud(np.swapaxes(np.swapaxes(DeepX, 0, 1), 1, 2)))
return DeepX
def _flirt_factory(self, name, to_reg, ref, reg, matrix, **kwargs):
"""
Registers a MR scan to a refernce MR scan using FSL's FLIRT command
Parameters
----------
name : str
Name for the generated pipeline
to_reg : str
Name of the DatasetSpec to register
ref : str
Name of the DatasetSpec to use as a reference
reg : str
Name of the DatasetSpec to output as registered image
matrix : str
Name of the DatasetSpec to output as registration matrix
"""
pipeline = self.create_pipeline(
name=name,
inputs=[
DatasetSpec(to_reg, nifti_gz_format),
DatasetSpec(ref, nifti_gz_format)
],
outputs=[
DatasetSpec(reg, nifti_gz_format),
DatasetSpec(matrix, text_matrix_format)
],
desc="Registers a MR scan against a reference image using FLIRT",
version=1,
citations=[fsl_cite],
**kwargs)
flirt = pipeline.create_node(interface=FLIRT(),
name='flirt',
requirements=[fsl5_req],
wall_time=5)
# Set registration parameters
flirt.inputs.dof = self.parameter('flirt_degrees_of_freedom')
flirt.inputs.cost = self.parameter('flirt_cost_func')
flirt.inputs.cost_func = self.parameter('flirt_cost_func')
flirt.inputs.output_type = 'NIFTI_GZ'
# Connect inputs
pipeline.connect_input(to_reg, flirt, 'in_file')
pipeline.connect_input(ref, flirt, 'reference')
# Connect outputs
pipeline.connect_output(reg, flirt, 'out_file')
pipeline.connect_output(matrix, flirt, 'out_matrix_file')
return pipeline
def make_w_masking():
w_mask = Workflow('masking')
n_in = Node(
IdentityInterface(fields=[
'T1w',
'subject', # without sub-
'freesurfer2func',
'func',
]),
name='input')
n_out = Node(IdentityInterface(fields=[
'func',
]), name='output')
n_fl = Node(FLIRT(), name='flirt')
n_fl.inputs.output_type = 'NIFTI_GZ'
n_fl.inputs.apply_xfm = True
n_fl.inputs.interp = 'nearestneighbour'
n_conv = Node(MRIConvert(), name='convert')
n_conv.inputs.out_type = 'niigz'
reconall = Node(ReconAll(), name='reconall')
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = '/Fridge/R01_BAIR/freesurfer'
w_mask.connect(n_in, 'T1w', reconall, 'T1_files')
w_mask.connect(n_in, 'subject', reconall, 'subject_id')
n_mul = Node(interface=BinaryMaths(), name='mul')
n_mul.inputs.operation = 'mul'
w_mask.connect(reconall, ('ribbon', select_ribbon), n_conv, 'in_file')
w_mask.connect(n_conv, 'out_file', n_fl, 'in_file')
w_mask.connect(n_in, 'func', n_fl, 'reference')
w_mask.connect(n_in, 'freesurfer2func', n_fl, 'in_matrix_file')
w_mask.connect(n_in, 'func', n_mul, 'in_file')
w_mask.connect(n_fl, 'out_file', n_mul, 'operand_file')
w_mask.connect(n_mul, 'out_file', n_out, 'func')
return w_mask
def run_t2w_deface(image, t1w_deface_mask, outfile):
from bidsonym.utils import deface_t2w
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']), name='inputnode')
flirtnode = pe.Node(FLIRT(cost_func='mutualinfo', output_type="NIFTI_GZ"))
deface_t2w = pe.Node(Function(
input_names=['image', 'warped_mask', 'outfile'],
output_names=['outfile'],
function=deface_t2w),
name='deface_t2w')
deface_wf.connect([(inputnode, flirtnode, [('in_file', 'reference')]),
(inputnode, deface_t2w, [('in_file', 'outfile')]),
(flirtnode, deface_t2w, [('out_file', 'warped_mask')])])
inputnode.inputs.in_file = image
flirtnode.inputs.in_file = t1w_deface_mask
deface_t2w.inputs.image = image
deface_wf.run()
def qform_transform_pipeline(self, **name_maps):
pipeline = self.new_pipeline(
name='qform_transform',
name_maps=name_maps,
desc="Registers a MR scan against a reference image",
references=[fsl_cite])
pipeline.add('flirt',
FLIRT(uses_qform=True, apply_xfm=True),
inputs={
'in_file': ('brain', nifti_gz_format),
'reference': ('coreg_ref_brain', nifti_gz_format)
},
outputs={
'out_file': ('qformed', nifti_gz_format),
'out_matrix_file': ('qform_mat', text_matrix_format)
},
requirements=[fsl_req.v('5.0.8')],
wall_time=5)
return pipeline
def wf_transform_anat(in_file_list, in_matrix_file_list, reference):
func2std_xform = MapNode(
FLIRT(output_type='NIFTI', apply_xfm=True),
name="func2std_xform",
iterfield=['in_file', 'in_matrix_file', 'reference'])
inputspec = Node(IdentityInterface(
fields=['in_file_list', 'in_matrix_file_list', 'reference']),
name="inputspec")
inputspec.inputs.in_file_list = in_file_list
inputspec.inputs.in_matrix_file_list = in_matrix_file_list
inputspec.inputs.reference = reference
wf_transform_anat = Workflow(name="wf_transform_anat")
wf_transform_anat.connect(inputspec, 'in_file_list', func2std_xform,
'in_file')
wf_transform_anat.connect(inputspec, 'in_matrix_file_list', func2std_xform,
'in_matrix_file')
wf_transform_anat.connect(inputspec, 'reference', func2std_xform,
'reference')
return wf_transform_anat
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})
"""
for i in range(len(path_t1)):
mask_ana(os.path.join(path_t1[i], "T1.nii"),
os.path.join(path_t1[i], "mask.nii"),
background_bright=False)
for i in range(len(path_epi)):
mask_epi(os.path.join(path_epi[i], "bepi.nii"),
os.path.join(path_t1[i], "pT1.nii"),
os.path.join(path_t1[i], "mask.nii"), niter_mask, sigma_mask,
file_cmap)
"""
flirt
"""
os.chdir(path_flirt)
flirt = FLIRT()
flirt.inputs.cost_func = "corratio"
flirt.inputs.dof = 6
flirt.inputs.interp = "trilinear" # trilinear, nearestneighbour, sinc or spline
flirt.inputs.in_file = os.path.join(path_epi_target, "pbepi.nii")
flirt.inputs.reference = os.path.join(path_epi_source, "pbepi.nii")
flirt.inputs.output_type = "NIFTI"
flirt.inputs.out_file = os.path.join(path_flirt, "flirt.nii")
flirt.inputs.out_matrix_file = os.path.join(path_flirt, "flirt_matrix.mat")
flirt.run()
"""
invert matrix
"""
invt = ConvertXFM()
invt.inputs.in_file = os.path.join(path_flirt, "flirt_matrix.mat")
invt.inputs.invert_xfm = True
def elecDetect(CT_dir, fs_dir,img, thresh_f, thresh_c, frac, num_gridStrips, n_elects):
# run CT_electhresh
print "::: Thresholding CT at %f stdv :::" %(thresh);
CT_img = CT_dir + img;
electhresh(CT_img,thresh_f, thresh_c);
# run im_filt to gaussian smooth thresholded image
fname = CT_dir + "thresh_" + img;
print "::: Applying guassian smooth of 2.5mm to thresh-CT :::";
img_filt(fname);
# compute hough transform to find electrode center coordinates
mlab = matlab.MatlabCommand();
mlab.inputs.script = "addpath(genpath('/Volumes/Thunderbolt_Duo/Scripts/Matlab/SphericalHough')); \
img = readFileNifti('%s/smoothed_thresh_CT.nii');img = img.data(); \
fltr4LM_R = 3; obj_cint = 0.0; radrange = [0.1, 3]; multirad = 0.3; \
grdthres = 0.33;\
[center_img,sphere_img,sphcen2,sphrad]=SphericalHough(img,radrange,grdthres, \
fltr4LM_R, multirad, obj_cint); save('%s/elec_spheres.mat', 'sphere_img'); \
save('%s/elec_centers.mat', 'center_img'); \
save('%s/3d_hough_elect_coords.mat', 'sphcen2');" %(CT_dir, CT_dir , CT_dir, CT_dir);
print "::: Applying 3D hough transform to smoothed thresh-CT :::";
out = mlab.run(); # run the hough and get errors if any ocur
# save txt version of hough putputs
coords = scipy.io.loadmat(CT_dir + '/'+ '3dHough_coords.mat').get('coords')
np.savetxt('dirty_elecsAll.txt', coords, delimiter=' ', fmt='%-7.1f');
# run fsl FLIRT to compute CT-MRI registration
flirt = FLIRT();
flirt.inputs.in_file = CT_dir + '/CT.nii';
flirt.inputs.reference = fs_dir + '/orig.nii';
flirt.inputs.cost_func = 'mutualinfo';
print "::: Computing corregistration between CT and MRI using FLIRT :::";
flirt.run();
# use fsl to calc voxel coords for elec centers in CT registered to orig
# in RAS voxel coordinates using affine from FLIRT
print "::: Applying FLIRT transformation to 3d Hough ouput :::";
orig_brain = fs_dir + '/orig.nii';
os.system('cat %s/dirty_elecsAll.txt | img2imgcoord -src %s/CT.nii -dest %s \
-xfm %s/CT_flirt.mat -vox > %s/dirty_elecsAll_RAS.txt' %(CT_dir, CT_dir, orig_brain, fs_dir, CT_dir));
# remove outliers caused by staples in the most superior portion of the img
print "::: Removing outliers from detected electrode coordinates :::";
elecs_dirty_RAS = scipy.loadtxt('dirty_elecsAll_RAS.txt', skiprows=1);
clean_elecs_RAS = [];
for i in elecs_dirty_RAS:
if i[1] > (0.3*np.max(elecs_dirty_RAS[:,2])):
clean_elecs_RAS.append(i);
clean_elecs_RAS = np.array(clean_elecs_RAS);
# save surface RAS coords for cleaned coords
# first apply vox2Ras affine for all fs orig volumes
print "::: Applying freesurfer vox2RAS transformation :::";
affine = np.array([[ -1., 0., 0., 128.],
[ 0., 0., 1., -128.],
[ 0., -1., 0., 128.],
[ 0., 0., 0., 1.]]);
intercept = np.ones(len(clean_elecs_RAS));
vox_elecs = np.column_stack((clean_elecs_RAS,intercept));
vox_elecs = np.transpose(vox_elecs);
sRAS_coords = np.matrix.dot(affine,vox_elecs);
sRAS_coords = np.transpose(sRAS_coords);
sRAS_coords = sRAS_coords[:,0:3];
# apply difference coord (lh_pial.asc - lh.pial) to shift all elecmatrix coords
c_RAS = get_cRAS(fs_dir,subj);
sRAS_coords = coords - c_RAS; # shifted to correct back to lh.pial coords
scipy.io.savemat('elecs_all_cleaned.mat', {'elecmatrix':sRAS_coords});
# run K means to find grid and strip clusters
n_clusts = num_gridStrips; # number of cluster to find = number of electrodes
iters = 1000;
init_clusts = n_clusts;
print "::: Performing K-means cluster to find %d grid-strip and noise clusters :::" %(n_clusts);
[clust_coords, clust_labels] = clust(sRAS_coords, n_clusts, iters, init_clusts);
# save cluster results as individual arrays
grid_strip_iter = np.linspace(0,num_gridStrips-1, num_gridStrips);
sRAS_coords_list = [list(b) for b in sRAS_coords];
clust_labels_list = list(clust_labels);
for i in grid_strip_iter:
coords = [];
for d in sRAS_coords_list:
if clust_labels_list[sRAS_coords_list.index(d)] == int(i):
coords.append(d);
coords = np.array(coords);
scipy.io.savemat('clust%s.mat' %(i), {'elecmatrix':coords});
def preproc(data_dir, sink_dir, subject, task, session, run, masks,
motion_thresh, moco):
from nipype.interfaces.fsl import MCFLIRT, FLIRT, FNIRT, ExtractROI, ApplyWarp, MotionOutliers, InvWarp, FAST
#from nipype.interfaces.afni import AlignEpiAnatPy
from nipype.interfaces.utility import Function
from nilearn.plotting import plot_anat
from nilearn import input_data
#WRITE A DARA GRABBER
def get_niftis(subject_id, data_dir, task, run, session):
from os.path import join, exists
t1 = join(data_dir, subject_id, 'session-{0}'.format(session),
'anatomical', 'anatomical-0', 'anatomical.nii.gz')
#t1_brain_mask = join(data_dir, subject_id, 'session-1', 'anatomical', 'anatomical-0', 'fsl', 'anatomical-bet.nii.gz')
epi = join(data_dir, subject_id, 'session-{0}'.format(session), task,
'{0}-{1}'.format(task, run), '{0}.nii.gz'.format(task))
assert exists(t1), "t1 does not exist at {0}".format(t1)
assert exists(epi), "epi does not exist at {0}".format(epi)
standard = '/home/applications/fsl/5.0.8/data/standard/MNI152_T1_2mm.nii.gz'
return t1, epi, standard
data = Function(
function=get_niftis,
input_names=["subject_id", "data_dir", "task", "run", "session"],
output_names=["t1", "epi", "standard"])
data.inputs.data_dir = data_dir
data.inputs.subject_id = subject
data.inputs.run = run
data.inputs.session = session
data.inputs.task = task
grabber = data.run()
if session == 0:
sesh = 'pre'
if session == 1:
sesh = 'post'
#reg_dir = '/home/data/nbc/physics-learning/data/first-level/{0}/session-1/retr/retr-{1}/retr-5mm.feat/reg'.format(subject, run)
#set output paths for quality assurance pngs
qa1 = join(
sink_dir, 'qa',
'{0}-session-{1}_{2}-{3}_t1_flirt.png'.format(subject, session, task,
run))
qa2 = join(
sink_dir, 'qa',
'{0}-session-{1}_{2}-{3}_mni_flirt.png'.format(subject, session, task,
run))
qa3 = join(
sink_dir, 'qa',
'{0}-session-{1}_{2}-{3}_mni_fnirt.png'.format(subject, session, task,
run))
confound_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_confounds.txt'.format(subject, session, task,
run))
#run motion correction if indicated
if moco == True:
mcflirt = MCFLIRT(ref_vol=144, save_plots=True, output_type='NIFTI_GZ')
mcflirt.inputs.in_file = grabber.outputs.epi
#mcflirt.inputs.in_file = join(data_dir, subject, 'session-1', 'retr', 'retr-{0}'.format(run), 'retr.nii.gz')
mcflirt.inputs.out_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mcf.nii.gz'.format(
subject, session, task, run))
flirty = mcflirt.run()
motion = np.genfromtxt(flirty.outputs.par_file)
else:
print "no moco needed"
motion = 0
#calculate motion outliers
try:
mout = MotionOutliers(metric='fd', threshold=motion_thresh)
mout.inputs.in_file = grabber.outputs.epi
mout.inputs.out_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_fd-gt-{3}mm'.format(
subject, session, task, run, motion_thresh))
mout.inputs.out_metric_plot = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_metrics.png'.format(
subject, session, task, run))
mout.inputs.out_metric_values = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_fd.txt'.format(subject, session, task,
run))
moutliers = mout.run()
outliers = np.genfromtxt(moutliers.outputs.out_file)
e = 'no errors in motion outliers, yay'
except Exception as e:
print(e)
outliers = np.genfromtxt(mout.inputs.out_metric_values)
#set everything above the threshold to 1 and everything below to 0
outliers[outliers > motion_thresh] = 1
outliers[outliers < motion_thresh] = 0
#concatenate motion parameters and motion outliers to form confounds file
#outliers = outliers.reshape((outliers.shape[0],1))
conf = outliers
np.savetxt(confound_file, conf, delimiter=',')
#extract an example volume for normalization
ex_fun = ExtractROI(t_min=144, t_size=1)
ex_fun.inputs.in_file = flirty.outputs.out_file
ex_fun.inputs.roi_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}-example_func.nii.gz'.format(
subject, session, task, run))
fun = ex_fun.run()
warp = ApplyWarp(interp="nn", abswarp=True)
if not exists(
'/home/data/nbc/physics-learning/data/first-level/{0}/session-{1}/{2}/{2}-{3}/{2}-5mm.feat/reg/example_func2standard_warp.nii.gz'
.format(subject, session, task, run)):
#two-step normalization using flirt and fnirt, outputting qa pix
flit = FLIRT(cost_func="corratio", dof=12)
reg_func = flit.run(
reference=fun.outputs.roi_file,
in_file=grabber.outputs.t1,
searchr_x=[-180, 180],
searchr_y=[-180, 180],
out_file=join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_t1-flirt.nii.gz'.format(
subject, session, task, run)),
out_matrix_file=join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_t1-flirt.mat'.format(
subject, session, task, run)))
reg_mni = flit.run(
reference=grabber.outputs.t1,
in_file=grabber.outputs.standard,
searchr_y=[-180, 180],
searchr_z=[-180, 180],
out_file=join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mni-flirt-t1.nii.gz'.format(
subject, session, task, run)),
out_matrix_file=join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mni-flirt-t1.mat'.format(
subject, session, task, run)))
#plot_stat_map(aligner.outputs.out_file, bg_img=fun.outputs.roi_file, colorbar=True, draw_cross=False, threshold=1000, output_file=qa1a, dim=-2)
display = plot_anat(fun.outputs.roi_file, dim=-1)
display.add_edges(reg_func.outputs.out_file)
display.savefig(qa1, dpi=300)
display.close()
display = plot_anat(grabber.outputs.t1, dim=-1)
display.add_edges(reg_mni.outputs.out_file)
display.savefig(qa2, dpi=300)
display.close()
perf = FNIRT(output_type='NIFTI_GZ')
perf.inputs.warped_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mni-fnirt-t1.nii.gz'.format(
subject, session, task, run))
perf.inputs.affine_file = reg_mni.outputs.out_matrix_file
perf.inputs.in_file = grabber.outputs.standard
perf.inputs.subsampling_scheme = [8, 4, 2, 2]
perf.inputs.fieldcoeff_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mni-fnirt-t1-warpcoeff.nii.gz'.format(
subject, session, task, run))
perf.inputs.field_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mni-fnirt-t1-warp.nii.gz'.format(
subject, session, task, run))
perf.inputs.ref_file = grabber.outputs.t1
reg2 = perf.run()
warp.inputs.field_file = reg2.outputs.field_file
#plot fnirted MNI overlaid on example func
display = plot_anat(grabber.outputs.t1, dim=-1)
display.add_edges(reg2.outputs.warped_file)
display.savefig(qa3, dpi=300)
display.close()
else:
warpspeed = InvWarp(output_type='NIFTI_GZ')
warpspeed.inputs.warp = '/home/data/nbc/physics-learning/data/first-level/{0}/session-{1}/{2}/{2}-{3}/{2}-5mm.feat/reg/example_func2standard_warp.nii.gz'.format(
subject, session, task, run)
warpspeed.inputs.reference = fun.outputs.roi_file
warpspeed.inputs.inverse_warp = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_mni-fnirt-t1-warp.nii.gz'.format(
subject, session, task, run))
mni2epiwarp = warpspeed.run()
warp.inputs.field_file = mni2epiwarp.outputs.inverse_warp
for key in masks.keys():
#warp takes us from mni to epi
warp.inputs.in_file = masks[key]
warp.inputs.ref_file = fun.outputs.roi_file
warp.inputs.out_file = join(
sink_dir, sesh, subject,
'{0}-session-{1}_{2}-{3}_{4}.nii.gz'.format(
subject, session, task, run, key))
net_warp = warp.run()
qa_file = join(
sink_dir, 'qa', '{0}-session-{1}_{2}-{3}_qa_{4}.png'.format(
subject, session, task, run, key))
display = plotting.plot_roi(net_warp.outputs.out_file,
bg_img=fun.outputs.roi_file,
colorbar=True,
vmin=0,
vmax=18,
draw_cross=False)
display.savefig(qa_file, dpi=300)
display.close()
return flirty.outputs.out_file, confound_file, e
# Skull Strip the fmri time series
bet_fmri_node = Node(BET(output_type='NIFTI', mask=True), name="bet_fmri")
# Bias Correct the fmri time series
bias_correction_node = Node(N4BiasFieldCorrection(), name='bias_correction')
# Returns the relative concentration of brain iron
rcfe_node = Node(Function(input_names=['input_image', 'mask_image'],
output_names=['output_image'],
function=compute_rcFe),
name="rcfe")
# coregister (skullstripped) mean of the fmri time series to the skull stripped T1 structural
flirt_node = Node(
FLIRT(dof=6), name="flirt",
cost='mutualinfo') #TODO: do i have to specify out_matrix_file???
# skullstrip the T1 structural image
skullstrip_structural_node = Node(SkullStrip(outputtype='NIFTI'),
name='skullstrip')
# coreg_to_struct_space = Node(FLIRT(apply_xfm=True, reference=struct_image, interp="sinc"), name="coreg")
coreg_to_struct_space_node = Node(FLIRT(apply_xfm=True,
interp="sinc",
cost='mutualinfo'),
name="coreg_to_struct_space")
# Warp whole head T1 Structural Image to MNI 152 template
warp_to_152_node = Node(legacy.GenWarpFields(similarity_metric="CC"),
name="warp152")
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})
write_bounding_box=[[-90, -126, -72], [90, 90, 108]]),
name="normalize_t1")
normalize_masks = Node(Normalize12(
jobtype='estwrite',
tpm=template,
write_voxel_sizes=[iso_size, iso_size, iso_size],
write_bounding_box=[[-90, -126, -72], [90, 90, 108]]),
name="normalize_masks")
# Threshold - Threshold WM probability image
threshold = Node(Threshold(thresh=0.5, args='-bin', output_type='NIFTI_GZ'),
name="wm_mask_threshold")
# FLIRT - pre-alignment of functional images to anatomical images
coreg_pre = Node(FLIRT(dof=6, output_type='NIFTI_GZ'),
name="linear_warp_estimation")
# FLIRT - coregistration of functional images to anatomical images with BBR
coreg_bbr = Node(FLIRT(dof=6,
cost='bbr',
schedule=opj(os.getenv('FSLDIR'),
'etc/flirtsch/bbr.sch'),
output_type='NIFTI_GZ'),
name="nonlinear_warp_estimation")
# Apply coregistration warp to functional images
applywarp = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI'),
name="registration_fmri")
def _fnirt_to_tmpl_pipeline(self, **name_maps):
"""
Registers a MR scan to a refernce MR scan using FSL's nonlinear FNIRT
command
Parameters
----------
template : Which template to use, can be one of 'mni_nl6'
"""
pipeline = self.new_pipeline(
name='mag_coreg_to_tmpl',
name_maps=name_maps,
desc=("Nonlinearly registers a MR scan to a standard space,"
"e.g. MNI-space"),
citations=[fsl_cite])
# Basic reorientation to standard MNI space
reorient = pipeline.add(
'reorient',
Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('mag_preproc', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')])
reorient_mask = pipeline.add(
'reorient_mask',
Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('brain_mask', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')])
reorient_brain = pipeline.add(
'reorient_brain',
Reorient2Std(
output_type='NIFTI_GZ'),
inputs={
'in_file': ('brain', nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')])
# Affine transformation to MNI space
flirt = pipeline.add(
'flirt',
interface=FLIRT(
dof=12,
output_type='NIFTI_GZ'),
inputs={
'reference': ('template_brain', nifti_gz_format),
'in_file': (reorient_brain, 'out_file')},
requirements=[fsl_req.v('5.0.8')],
wall_time=5)
# Apply mask if corresponding subsampling scheme is 1
# (i.e. 1-to-1 resolution) otherwise don't.
apply_mask = [int(s == 1)
for s in self.parameter('fnirt_subsampling')]
# Nonlinear transformation to MNI space
pipeline.add(
'fnirt',
interface=FNIRT(
output_type='NIFTI_GZ',
intensity_mapping_model=(
self.parameter('fnirt_intensity_model')
if self.parameter('fnirt_intensity_model') is not None else
'none'),
subsampling_scheme=self.parameter('fnirt_subsampling'),
fieldcoeff_file=True,
in_fwhm=[8, 6, 5, 4, 3, 2], # [8, 6, 5, 4.5, 3, 2] This threw an error because of float value @IgnorePep8,
ref_fwhm=[8, 6, 5, 4, 2, 0],
regularization_lambda=[300, 150, 100, 50, 40, 30],
apply_intensity_mapping=[1, 1, 1, 1, 1, 0],
max_nonlin_iter=[5, 5, 5, 5, 5, 10],
apply_inmask=apply_mask,
apply_refmask=apply_mask),
inputs={
'ref_file': ('template', nifti_gz_format),
'refmask': ('template_mask', nifti_gz_format),
'in_file': (reorient, 'out_file'),
'inmask_file': (reorient_mask, 'out_file'),
'affine_file': (flirt, 'out_matrix_file')},
outputs={
'mag_coreg_to_tmpl': ('warped_file', nifti_gz_format),
'coreg_to_tmpl_fsl_coeff': ('fieldcoeff_file',
nifti_gz_format)},
requirements=[fsl_req.v('5.0.8')],
wall_time=60)
# Set registration parameters
# TODO: Need to work out which parameters to use
return pipeline
import os
from os.path import abspath
from datetime import datetime
from IPython.display import Image
import pydot
from nipype import Workflow, Node, MapNode, Function, config
from nipype.interfaces.fsl import TOPUP, ApplyTOPUP, BET, ExtractROI, Eddy, FLIRT, FUGUE
from nipype.interfaces.fsl.maths import MathsCommand
import nipype.interfaces.utility as util
import nipype.interfaces.mrtrix3 as mrt
#Requirements for the workflow to run smoothly: All files as in NIfTI-format and named according to the following standard:
#Images are from the tonotopy DKI sequences on the 7T Philips Achieva scanner in Lund. It should work with any DKI sequence and possibly also a standard DTI but the setting for B0-corrections, epi-distortion corrections and eddy current corrections will be wrong.
#DKI file has a base name shared with bvec and bval in FSL format. E.g. "DKI.nii.gz" "DKI.bvec" and "DKI.bval".
#There is one b0-volume with reversed (P->A) phase encoding called DKIbase+_revenc. E.g. "DKI_revenc.nii.gz".
#Philips B0-map magnitude and phase offset (in Hz) images.
#One input file for topup describing the images as specified by topup.
#Set nbrOfThreads to number of available CPU threads to run the analyses.
### Need to make better revenc for the 15 version if we choose to use it (i.e. same TE and TR)
#Set to relevant directory/parameters
datadir=os.path.abspath("/Users/ling-men/Documents/MRData/testDKI")
rawDKI_base='DKI_15'
B0map_base = 'B0map'
nbrOfThreads=6
print_graph = True
acqparam_file = os.path.join(datadir,'acqparams.txt')
index_file = os.path.join(datadir,'index.txt')
####
#config.enable_debug_mode()
DKI_nii=os.path.join(datadir, rawDKI_base+'.nii.gz')
DKI_bval=os.path.join(datadir, rawDKI_base+'.bval')