def init_fsl(self, in_file: str, ref: str, out_file: str, field_file: str):
aw = fsl.ApplyWarp()
aw.inputs.in_file = in_file
aw.inputs.out_file = out_file
aw.inputs.field_file = field_file
aw.inputs.ref_file = ref
return aw
def func2mni_wf():
mni_skull_2mm = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm.nii.gz'
mni_brain_2mm = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
flow = Workflow('func2mni_nonlinear')
inputnode = Node(util.IdentityInterface(fields=['func_image',
'reference_image',
'func2anat_affine',
'anat2mni_warp']),name = 'inputnode')
outputnode = Node(util.IdentityInterface(fields=['func2mni_2mm',
'func2mni_4mm']),name = 'outputnode')
applywarp = Node(fsl.ApplyWarp(), name = 'apply_warp',)
applywarp.inputs.ref_file = mni_brain_2mm
flirt4mm = Node(fsl.FLIRT(), name = 'resample_4mm')
flirt4mm.inputs.reference = mni_brain_2mm
flirt4mm.inputs.apply_isoxfm = 4.0
flow.connect(inputnode, 'func_image' , applywarp, 'in_file')
flow.connect(inputnode, 'anat2mni_warp' , applywarp, 'field_file')
flow.connect(inputnode, 'func2anat_affine' , applywarp, 'premat')
flow.connect(applywarp, 'out_file' , flirt4mm, 'in_file')
flow.connect(applywarp, 'out_file' , outputnode, 'func2mni_2mm')
flow.connect(flirt4mm, 'out_file' , outputnode, 'func2mni_4mm')
return flow
def apply_warp(
in_file: Path, ref: Path, warp: Path, out_file: Path, interp: str = None
):
"""
Apply pre-calculated warp field coefficients to normalize an image.
Parameters
----------
in_file : Path
Path to image to be normalized
ref : Path
Path to reference image
warp : Path
Path to pre-calculated warp field
out_file : Path
Path to output warped image
"""
aw = fsl.ApplyWarp()
aw.inputs.in_file = in_file
aw.inputs.ref_file = ref
aw.inputs.field_file = warp
aw.inputs.out_file = out_file
if interp:
aw.inputs.interp = interp
return aw
def create_templates_2func_workflow(threshold=0.5,
name='templates_2func_workflow'):
templates_2func_workflow = Workflow(name=name)
# Input Node
inputspec = Node(utility.IdentityInterface(fields=[
'func_file',
'premat',
'warp',
'templates',
]),
name='inputspec')
# Get the overal EPI to MNI warp
func_2mni_warp = Node(fsl.ConvertWarp(), name='func_2mni_warp')
func_2mni_warp.inputs.reference = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
# Calculate the inverse warp
mni_2func_warp = Node(fsl.InvWarp(), name='mni_2func_warp')
# Transform MNI templates to EPI space
templates_2func_apply = MapNode(fsl.ApplyWarp(),
iterfield=['in_file'],
name='templates_2func_apply')
# Threshold templates
templates_threshold = MapNode(
fsl.ImageMaths(op_string='-thr {0} -bin'.format(threshold)),
iterfield=['in_file'],
name='templates_threshold')
# Output Node
outputspec = Node(utility.IdentityInterface(
fields=['templates_2func_files', 'func_2mni_warp']),
name='outputspec')
# Connect the workflow nodes
templates_2func_workflow.connect(inputspec, 'premat', func_2mni_warp,
'premat')
templates_2func_workflow.connect(inputspec, 'warp', func_2mni_warp,
'warp1')
templates_2func_workflow.connect(inputspec, 'func_file', mni_2func_warp,
'reference')
templates_2func_workflow.connect(func_2mni_warp, 'out_file',
mni_2func_warp, 'warp')
templates_2func_workflow.connect(inputspec, 'templates',
templates_2func_apply, 'in_file')
templates_2func_workflow.connect(inputspec, 'func_file',
templates_2func_apply, 'ref_file')
templates_2func_workflow.connect(mni_2func_warp, 'inverse_warp',
templates_2func_apply, 'field_file')
templates_2func_workflow.connect(templates_2func_apply, 'out_file',
templates_threshold, 'in_file')
templates_2func_workflow.connect(func_2mni_warp, 'out_file', outputspec,
'func_2mni_warp')
templates_2func_workflow.connect(templates_threshold, 'out_file',
outputspec, 'templates_2func_files')
return templates_2func_workflow
def create_normalize_workflow(name="normalize"):
# Define the workflow inputs
inputnode = pe.Node(util.IdentityInterface(
fields=["timeseries", "flirt_affine", "warpfield"]),
name="inputs")
# Define the target space and warp to it
mni152 = fsl.Info.standard_image("avg152T1_brain.nii.gz")
applywarp = pe.MapNode(fsl.ApplyWarp(ref_file=mni152, interp="spline"),
iterfield=["in_file", "premat"],
name="applywarp")
# Rename the timeseries
rename = pe.MapNode(util.Rename(format_string="timeseries_warped",
keep_ext=True),
iterfield=["in_file"],
name="rename")
# Define the outputs
outputnode = pe.Node(util.IdentityInterface(fields=["timeseries"]),
name="outputs")
normalize = pe.Workflow(name=name)
normalize.connect([
(inputnode, applywarp, [("timeseries", "in_file"),
("warpfield", "field_file"),
("flirt_affine", "premat")]),
(applywarp, rename, [("out_file", "in_file")]),
(rename, outputnode, [("out_file", "timeseries")]),
])
return normalize
def test_nonlinear_register():
from ..registration import create_nonlinear_register
from CPAC.pipeline import nipype_pipeline_engine as pe
import nipype.interfaces.fsl as fsl
## necessary inputs
## -input_brain
## -input_skull
## -reference_brain
## -reference_skull
## -fnirt_config
## -fnirt_warp_res
## input_brain
anat_bet_file = '/home/data/Projects/nuisance_reliability_paper/working_dir_CPAC_order/resting_preproc/anatpreproc/_session_id_NYU_TRT_session1_subject_id_sub05676/anat_skullstrip/mprage_anonymized_RPI_3dT.nii.gz'
## input_skull
## reference_brain
mni_file = '/usr/share/fsl/4.1/data/standard/MNI152_T1_3mm_brain.nii.gz'
## reference_skull
## fnirt_config
fnirt_config = 'T1_2_MNI152_3mm'
## fnirt_warp_res
fnirt_warp_res = None
#?? what is this for?:
func_file = '/home/data/Projects/nuisance_reliability_paper/working_dir_CPAC_order/resting_preproc/nuisance_preproc/_session_id_NYU_TRT_session1_subject_id_sub05676/_csf_threshold_0.4/_gm_threshold_0.2/_wm_threshold_0.66/_run_scrubbing_False/_nc_5/_selector_6.7/regress_nuisance/mapflow/_regress_nuisance0/residual.nii.gz'
mni_workflow = pe.Workflow(name='mni_workflow')
linear_reg = pe.Node(interface=fsl.FLIRT(), name='linear_reg_0')
linear_reg.inputs.cost = 'corratio'
linear_reg.inputs.dof = 6
linear_reg.inputs.interp = 'nearestneighbour'
linear_reg.inputs.in_file = func_file
linear_reg.inputs.reference = anat_bet_file
#T1 to MNI Node
c = create_nonlinear_register()
c.inputs.inputspec.input = anat_bet_file
c.inputs.inputspec.reference = '/usr/share/fsl/4.1/data/standard/MNI152_T1_3mm_brain.nii.gz'
c.inputs.inputspec.fnirt_config = 'T1_2_MNI152_3mm'
#EPI to MNI warp Node
mni_warp = pe.Node(interface=fsl.ApplyWarp(), name='mni_warp')
mni_warp.inputs.ref_file = '/usr/share/fsl/4.1/data/standard/MNI152_T1_3mm_brain.nii.gz'
mni_warp.inputs.in_file = func_file
mni_workflow.connect(c, 'outputspec.nonlinear_xfm', mni_warp, 'field_file')
mni_workflow.connect(linear_reg, 'out_matrix_file', mni_warp, 'premat')
mni_workflow.base_dir = './'
mni_workflow.run()
def apply_all_corrections(name='UnwarpArtifacts'):
"""
Combines two lists of linear transforms with the deformation field
map obtained typically after the SDC process.
Additionally, computes the corresponding bspline coefficients and
the map of determinants of the jacobian.
"""
inputnode = pe.Node(niu.IdentityInterface(fields=['in_sdc',
'in_hmc', 'in_ecc', 'in_dwi']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['out_file', 'out_warp',
'out_coeff', 'out_jacobian']), name='outputnode')
warps = pe.MapNode(fsl.ConvertWarp(relwarp=True),
iterfield=['premat', 'postmat'],
name='ConvertWarp')
selref = pe.Node(niu.Select(index=[0]), name='Reference')
split = pe.Node(fsl.Split(dimension='t'), name='SplitDWIs')
unwarp = pe.MapNode(fsl.ApplyWarp(), iterfield=['in_file', 'field_file'],
name='UnwarpDWIs')
coeffs = pe.MapNode(fsl.WarpUtils(out_format='spline'),
iterfield=['in_file'], name='CoeffComp')
jacobian = pe.MapNode(fsl.WarpUtils(write_jacobian=True),
iterfield=['in_file'], name='JacobianComp')
jacmult = pe.MapNode(fsl.MultiImageMaths(op_string='-mul %s'),
iterfield=['in_file', 'operand_files'],
name='ModulateDWIs')
thres = pe.MapNode(fsl.Threshold(thresh=0.0), iterfield=['in_file'],
name='RemoveNegative')
merge = pe.Node(fsl.Merge(dimension='t'), name='MergeDWIs')
wf = pe.Workflow(name=name)
wf.connect([
(inputnode, warps, [('in_sdc', 'warp1'),
('in_hmc', 'premat'),
('in_ecc', 'postmat'),
('in_dwi', 'reference')]),
(inputnode, split, [('in_dwi', 'in_file')]),
(split, selref, [('out_files', 'inlist')]),
(warps, unwarp, [('out_file', 'field_file')]),
(split, unwarp, [('out_files', 'in_file')]),
(selref, unwarp, [('out', 'ref_file')]),
(selref, coeffs, [('out', 'reference')]),
(warps, coeffs, [('out_file', 'in_file')]),
(selref, jacobian, [('out', 'reference')]),
(coeffs, jacobian, [('out_file', 'in_file')]),
(unwarp, jacmult, [('out_file', 'in_file')]),
(jacobian, jacmult, [('out_jacobian', 'operand_files')]),
(jacmult, thres, [('out_file', 'in_file')]),
(thres, merge, [('out_file', 'in_files')]),
(warps, outputnode, [('out_file', 'out_warp')]),
(coeffs, outputnode, [('out_file', 'out_coeff')]),
(jacobian, outputnode, [('out_jacobian', 'out_jacobian')]),
(merge, outputnode, [('merged_file', 'out_file')])
])
return wf
def _run_interface(self, runtime):
for in_file in self.inputs.in_files:
ax = fsl.ApplyWarp(in_file=in_file,
interp=self.inputs.interp,
field_file=self.inputs.field_file,
ref_file=self.inputs.ref_file)
ax.run()
return runtime
def preprocess_and_tmp_save_fmri(data_path,
task,
subj,
model,
tmp_path,
group_mask=None):
'''
Generator for preprocessed fMRI runs from one subject of Forrest Gump
aligns to group template
run-wise linear de-trending and z-scoring
IN:
data_path - string, path pointing to the Forrest Gump directory
task - string, which part of the Forrest Gump dataset to load
subj - int, subject to pre-process
tmp_path - string, path to save the dataset temporarily to
OUT:
preprocessed fMRI samples per run'''
from nipype.interfaces import fsl
dhandle = mvpa.OpenFMRIDataset(data_path)
flavor = 'dico_bold7Tp1_to_subjbold7Tp1'
if group_mask is None:
group_mask = os.path.join(data_path, 'sub{0:03d}'.format(subj),
'templates', 'bold7Tp1', 'in_grpbold7Tp1',
'brain_mask.nii.gz')
mask_fname = os.path.join(data_path, 'sub{0:03d}'.format(subj),
'templates', 'bold7Tp1', 'brain_mask.nii.gz')
for run_id in dhandle.get_task_bold_run_ids(task)[subj]:
run_ds = dhandle.get_bold_run_dataset(subj,
task,
run_id,
chunks=run_id - 1,
mask=mask_fname,
flavor=flavor)
filename = 'brain_subj_{}_run_{}.nii.gz'.format(subj, run_id)
tmp_file = os.path.join(tmp_path, filename)
save(unmask(run_ds.samples.astype('float32'), mask_fname), tmp_file)
warp = fsl.ApplyWarp()
warp.inputs.in_file = tmp_file
warp.inputs.out_file = os.path.join(tmp_path, 'group_' + filename)
warp.inputs.ref_file = os.path.join(data_path, 'templates',
'grpbold7Tp1', 'brain.nii.gz')
warp.inputs.field_file = os.path.join(data_path,
'sub{0:03d}'.format(subj),
'templates', 'bold7Tp1',
'in_grpbold7Tp1',
'subj2tmpl_warp.nii.gz')
warp.inputs.interp = 'nn'
warp.run()
os.remove(tmp_file)
run_ds = mvpa.fmri_dataset(os.path.join(tmp_path, 'group_' + filename),
mask=group_mask,
chunks=run_id - 1)
mvpa.poly_detrend(run_ds, polyord=1)
mvpa.zscore(run_ds)
os.remove(os.path.join(tmp_path, 'group_' + filename))
yield run_ds.samples.astype('float32')
def create_realign_flow(name='realign'):
"""Realign a time series to the middle volume using spline interpolation
Uses MCFLIRT to realign the time series and ApplyWarp to apply the rigid
body transformations using spline interpolation (unknown order).
Example
-------
>>> wf = create_realign_flow()
>>> wf.inputs.inputspec.func = 'f3.nii'
>>> wf.run() # doctest: +SKIP
"""
realignflow = pe.Workflow(name=name)
inputnode = pe.Node(interface=util.IdentityInterface(fields=[
'func',
]),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(
fields=['realigned_file', 'rms_files', 'par_file']),
name='outputspec')
start_dropper = pe.Node(util.Function(
input_names=['in_vol_fn', 'n_frames'],
output_names=['out_fn'],
function=remove_first_n_frames),
name='start_dropper')
start_dropper.inputs.n_frames = 5
realigner = pe.Node(fsl.MCFLIRT(save_mats=True,
stats_imgs=True,
save_rms=True,
save_plots=True),
name='realigner')
splitter = pe.Node(fsl.Split(dimension='t'), name='splitter')
warper = pe.MapNode(fsl.ApplyWarp(interp='spline'),
iterfield=['in_file', 'premat'],
name='warper')
joiner = pe.Node(fsl.Merge(dimension='t'), name='joiner')
realignflow.connect(inputnode, 'func', start_dropper, 'in_vol_fn')
realignflow.connect(start_dropper, 'out_fn', realigner, 'in_file')
realignflow.connect(start_dropper, ('out_fn', select_volume, 'middle'),
realigner, 'ref_vol')
realignflow.connect(realigner, 'out_file', splitter, 'in_file')
realignflow.connect(realigner, 'mat_file', warper, 'premat')
realignflow.connect(realigner, 'variance_img', warper, 'ref_file')
realignflow.connect(splitter, 'out_files', warper, 'in_file')
realignflow.connect(warper, 'out_file', joiner, 'in_files')
realignflow.connect(joiner, 'merged_file', outputnode, 'realigned_file')
realignflow.connect(realigner, 'rms_files', outputnode, 'rms_files')
realignflow.connect(realigner, 'par_file', outputnode, 'par_file')
return realignflow
def apply_warp(in_file: Path, ref: Path, warp: Path, out_file: Path):
"""
Apply non-linear warp file in an image to resample it to another one
Arguments:
in_file {Path} -- [Image to apply non-linear warp on]
ref {Path} -- [Image to resample to]
warp {Path} -- [non-linear warp file]
out_file {Path} -- [Output image]
"""
aw = fsl.ApplyWarp()
aw.inputs.in_file = in_file
aw.inputs.ref_file = ref
aw.inputs.field_file = warp
aw.inputs.out_file = out_file
return aw
def CBF_modulation_( self, CBF_dir ):
"""CBF applyed GM Modulation."""
try:
#
#
# Loop on the tasks
while True:
# get the item
item = self.queue_CBF_.get()
# find the corresponding GM
GM_warp_coeff = "%s_non_li_template_coeff.nii.gz"%(item[4:-7])
GM_warp_jac = "%s_non_li_template_jac.nii.gz"%(item[4:-7])
# apply the GM warp
aw = fsl.ApplyWarp()
aw.inputs.in_file = os.path.join(CBF_dir, item )
aw.inputs.ref_file = self.template_
aw.inputs.out_file = os.path.join( self.template_dir_,
"%s_non_li_template_warped.nii.gz"%item[:-7] )
aw.inputs.field_file = os.path.join( self.template_dir_, GM_warp_coeff )
res = aw.run()
# Modulate with the GM jacobian
maths = fsl.ImageMaths()
maths.inputs.in_file = os.path.join(self.template_dir_,
"%s_non_li_template_warped.nii.gz"%item[:-7])
maths.inputs.op_string = '-mul %s'%( os.path.join(self.template_dir_, GM_warp_jac) )
maths.inputs.out_file = os.path.join( self.template_dir_,
"%s_modulated.nii.gz"%item[:-7] )
maths.inputs.out_data_type = "float"
maths.run();
# lock and add the file
singlelock.acquire()
self.CBF_warped_template_.append( aw.inputs.out_file )
self.CBF_modulated_template_.append( maths.inputs.out_file )
singlelock.release()
# job is done
self.queue_CBF_.task_done()
#
#
except Exception as inst:
print inst
_log.error(inst)
quit(-1)
except IOError as e:
print "I/O error({0}): {1}".format(e.errno, e.strerror)
quit(-1)
except:
print "Unexpected error:", sys.exc_info()[0]
quit(-1)
def create_normalization_wf(transformations=["mni2func"]):
wf = pe.Workflow(name="normalization")
inputspec = pe.Node(util.IdentityInterface(fields=[
'T1', 'skullstripped_T1', 'preprocessed_epi', 'func2anat_transform'
]),
name="inputspec")
anat2mni = create_nonlinear_register("anat2mni")
linear_reg = anat2mni.get_node("linear_reg_0")
linear_reg.inputs.searchr_x = [-180, 180]
linear_reg.inputs.searchr_y = [-180, 180]
linear_reg.inputs.searchr_z = [-180, 180]
skull_mgz2nii = pe.Node(fs.MRIConvert(out_type="nii"),
name="skull_mgs2nii")
brain_mgz2nii = skull_mgz2nii.clone(name="brain_mgs2nii")
wf.connect(inputspec, "skullstripped_T1", brain_mgz2nii, "in_file")
wf.connect(inputspec, "T1", skull_mgz2nii, "in_file")
anat2mni.inputs.inputspec.reference_skull = fsl.Info.standard_image(
"MNI152_T1_2mm.nii.gz")
anat2mni.inputs.inputspec.reference_brain = fsl.Info.standard_image(
"MNI152_T1_2mm_brain.nii.gz")
anat2mni.inputs.inputspec.fnirt_config = "T1_2_MNI152_2mm"
wf.connect(skull_mgz2nii, "out_file", anat2mni, "inputspec.input_skull")
wf.connect(brain_mgz2nii, "out_file", anat2mni, "inputspec.input_brain")
if 'mni2func' in transformations:
invert_warp = pe.Node(fsl.InvWarp(), name="invert_warp")
wf.connect(anat2mni, "outputspec.nonlinear_xfm", invert_warp,
"warp_file")
wf.connect(skull_mgz2nii, "out_file", invert_warp, "ref_file")
if 'func2mni' in transformations:
mni_warp = pe.Node(interface=fsl.ApplyWarp(), name='mni_warp')
mni_warp.inputs.ref_file = fsl.Info.standard_image(
"MNI152_T1_2mm.nii.gz")
wf.connect(inputspec, 'preprocessed_epi', mni_warp, 'in_file')
wf.connect(anat2mni, 'outputspec.nonlinear_xfm', mni_warp,
'field_file')
wf.connect(inputspec, 'func2anat_transform', mni_warp, 'premat')
return wf
def apply_warp(in_file,
ref_file,
field_file,
output_dir,
recalculate=False,
**kwargs):
"""Wrapper for the Nipype FSL applywarp wrapper.
Please remember to set the kwarg interp='nn' if you are warping a file with discrete ROI's.
Args:
in_file: image to be warped
ref_file: the reference image
field_file: file containing warp field (this is the --warp parameter from FSL applywarp)
output_dir: the output directory
recalculate (boolean): if we recalculate if the output already exists. Set this to False to easily get the
output easily.
**kwargs: extra arguments for the Nipype FSL applywarp
Returns:
dict: location of the output files:
- warped_image: the path to the output image.
"""
output_file = os.path.join(output_dir,
'warped_' + os.path.basename(in_file))
output = {'warped_image': output_file}
if not recalculate and os.path.isfile(output_file):
return output
aw = fsl.ApplyWarp(**kwargs)
aw.inputs.in_file = in_file
aw.inputs.ref_file = ref_file
aw.inputs.field_file = field_file
aw.inputs.out_file = output_file
applywarp = pe.Node(aw, name='applywarp')
applywarp.base_dir = os.path.join(output_dir, '_nipype_work_dir')
applywarp.run()
return output
def apply_warp_( self, Dir_list ):
"""."""
try:
#
#
#
# Loop on the tasks
while True:
# get the item
item = os.path.join( Dir_list, self.queue_warp_.get() )
#
# Find the matching T1 image
PIDN = [int(s) for s in item.split("_") if s.isdigit()]
#
warping_coeff = [ s for s in os.listdir(self.template_dir_) if str(PIDN[0]) in s
and "template_coeff" in s]
# Warp the brain
aw = fsl.ApplyWarp()
aw.inputs.in_file = item
aw.inputs.ref_file = self.template_
aw.inputs.out_file = "%s_MNI.nii.gz"%item[:-7]
aw.inputs.field_file = os.path.join( self.template_dir_, warping_coeff[0] )
res = aw.run()
# job is done
self.queue_warp_.task_done()
#
#
except Exception as inst:
print inst
_log.error(inst)
quit(-1)
except IOError as e:
print "I/O error({0}): {1}".format(e.errno, e.strerror)
quit(-1)
except:
print "Unexpected error:", sys.exc_info()[0]
quit(-1)
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['brain', 'label-reorient_T1w']]:
# TODO: disable skullstrip
linear_reg = NipypeJob(interface=fsl.FLIRT(cost='corratio'),
reference='linear_reg_0')
inv_flirt_xfm = NipypeJob(
interface=fsl.utils.ConvertXFM(invert_xfm=True),
reference='inv_linear_reg0_xfm')
linear_reg.in_file = rp[R('brain')]
linear_reg.reference = config.template_brain
linear_reg.interp = config.interpolation
inv_flirt_xfm.in_file = linear_reg.out_matrix_file
if config.linear_only:
rp[R('brain', space='MNI')] = linear_reg.out_file
# other xfm
return
else:
nonlinear_reg = NipypeJob(interface=fsl.FNIRT(fieldcoeff_file=True,
jacobian_file=True),
reference='nonlinear_reg_1')
brain_warp = NipypeJob(interface=fsl.ApplyWarp(),
reference='brain_warp')
nonlinear_reg.in_file = rp[R('T1w', label='reorient')]
nonlinear_reg.ref_file = config.template_skull
nonlinear_reg.refmask_file = config.ref_mask
nonlinear_reg.config_file = config.fnirt_config
nonlinear_reg.affine_file = linear_reg.out_matrix_file
brain_warp.interp = config.interpolation
brain_warp.in_file = rp[R('brain')]
brain_warp.field_file = nonlinear_reg.fieldcoeff_file
brain_warp.ref_file = config.template_brain
rp[R('brain', space='MNI')] = brain_warp.out_file
def create_indnet_workflow(hp_cutoff=100,
smoothing=5,
smm_threshold=0.5,
binarise_threshold=0.5,
melodic_seed=None,
aggr_aroma=False,
name="indnet"):
indnet = Workflow(name=name)
# Input node
inputspec = Node(utility.IdentityInterface(
fields=['anat_file', 'func_file', 'templates', 'networks']),
name='inputspec')
# T1 skullstrip
anat_bet = Node(fsl.BET(), name="anat_bet")
# EPI preprocessing
func_realignsmooth = create_featreg_preproc(highpass=False,
whichvol='first',
name='func_realignsmooth')
func_realignsmooth.inputs.inputspec.fwhm = smoothing
# Transform EPI to MNI space
func_2mni = create_reg_workflow(name='func_2mni')
func_2mni.inputs.inputspec.target_image = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
func_2mni.inputs.inputspec.target_image_brain = fsl.Info.standard_image(
'MNI152_T1_2mm_brain.nii.gz')
func_2mni.inputs.inputspec.config_file = 'T1_2_MNI152_2mm'
# Segmentation of T1
anat_segmentation = Node(fsl.FAST(output_biascorrected=True),
name='anat_segmentation')
# Transfrom segments to EPI space
segments_2func = create_segments_2func_workflow(
threshold=binarise_threshold, name='segments_2func')
# Transform templates to EPI space
templates_2func = create_templates_2func_workflow(
threshold=binarise_threshold, name='templates_2func')
# Mask network templates with GM
gm_mask_templates = MapNode(fsl.ImageMaths(op_string='-mul'),
iterfield=['in_file2'],
name='gm_mask_templates')
# Mask for ICA-AROMA and statistics
func_brainmask = Node(fsl.BET(frac=0.3,
mask=True,
no_output=True,
robust=True),
name='func_brainmask')
# Melodic ICA
if melodic_seed != None:
func_melodic = Node(fsl.MELODIC(args='--seed={}'.format(melodic_seed),
out_stats=True),
name='func_melodic')
# ICA-AROMA
func_aroma = Node(fsl.ICA_AROMA(), name='func_aroma')
if aggr_aroma:
func_aroma.inputs.denoise_type = 'aggr'
else:
func_aroma.inputs.denoise_type = 'nonaggr'
# Highpass filter ICA results
func_highpass = create_highpass_filter(cutoff=hp_cutoff,
name='func_highpass')
# Calculate mean CSF sgnal
csf_meansignal = Node(fsl.ImageMeants(), name='csf_meansignal')
# Calculate mean WM signal
wm_meansignal = Node(fsl.ImageMeants(), name='wm_meansignal')
# Calculate mean non-brain signal
nonbrain_meansignal = create_nonbrain_meansignal(
name='nonbrain_meansignal')
# Calculate first Eigenvariates
firsteigenvariates = MapNode(fsl.ImageMeants(show_all=True, eig=True),
iterfield=['mask'],
name='firsteigenvariates')
# Combine first eigenvariates and wm/csf/non-brain signals
regressors = Node(utility.Merge(4), name='regressors')
# z-transform regressors
ztransform = MapNode(Ztransform(),
iterfield=['in_file'],
name='ztransform')
# Create design matrix
designmatrix = Node(DesignMatrix(), name='designmatrix')
# Create contrasts
contrasts = Node(Contrasts(), name='contrasts')
# GLM
glm = Node(fsl.GLM(), name='glm')
glm.inputs.out_z_name = 'z_stats.nii.gz'
glm.inputs.demean = True
# Split z-maps
zmaps = Node(fsl.Split(), name='zmaps')
zmaps.inputs.dimension = 't'
# Spatial Mixture Modelling
smm = MapNode(fsl.SMM(), iterfield=['spatial_data_file'], name='smm')
# Transform probability maps to native (anat) space
actmaps_2anat = MapNode(fsl.ApplyXFM(),
iterfield=['in_file'],
name='actmaps_2anat')
# Transform probability maps to MNI space
actmaps_2mni = MapNode(fsl.ApplyWarp(),
iterfield=['in_file'],
name='actmaps_2mni')
actmaps_2mni.inputs.ref_file = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
# Create network masks in native (func) space
network_masks_func = create_network_masks_workflow(
name='network_masks_func', smm_threshold=smm_threshold)
# Create network masks in native (anat) space
network_masks_anat = create_network_masks_workflow(
name='network_masks_anat', smm_threshold=smm_threshold)
# Create network masks in MNI space
network_masks_mni = create_network_masks_workflow(
name='network_masks_mni', smm_threshold=smm_threshold)
# Output node
outputspec = Node(utility.IdentityInterface(fields=[
'network_masks_func_main', 'network_masks_func_exclusive',
'network_masks_anat_main', 'network_masks_anat_exclusive',
'network_masks_mni_main', 'network_masks_mni_exclusive',
'preprocessed_func_file', 'preprocessed_anat_file',
'motion_parameters', 'func2anat_transform', 'anat2mni_transform'
]),
name='outputspec')
# Helper functions
def get_first_item(x):
try:
return x[0]
except:
return x
def get_second_item(x):
return x[1]
def get_third_item(x):
return x[2]
def get_components(x):
return [y['components'] for y in x]
# Connect the nodes
# anat_bet
indnet.connect(inputspec, 'anat_file', anat_bet, 'in_file')
# func_realignsmooth
indnet.connect(inputspec, 'func_file', func_realignsmooth,
'inputspec.func')
# func_2mni
indnet.connect(func_realignsmooth,
('outputspec.smoothed_files', get_first_item), func_2mni,
'inputspec.source_files')
indnet.connect(inputspec, 'anat_file', func_2mni,
'inputspec.anatomical_image')
indnet.connect(func_realignsmooth, 'outputspec.reference', func_2mni,
'inputspec.mean_image')
# anat_segmentation
indnet.connect(anat_bet, 'out_file', anat_segmentation, 'in_files')
# segments_2func
indnet.connect(anat_segmentation, 'partial_volume_files', segments_2func,
'inputspec.segments')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', segments_2func,
'inputspec.premat')
indnet.connect(func_realignsmooth, 'outputspec.mean', segments_2func,
'inputspec.func_file')
# templates_2func
indnet.connect(func_realignsmooth, 'outputspec.mean', templates_2func,
'inputspec.func_file')
indnet.connect(func_2mni, 'outputspec.func2anat_transform',
templates_2func, 'inputspec.premat')
indnet.connect(func_2mni, 'outputspec.anat2target_transform',
templates_2func, 'inputspec.warp')
indnet.connect(inputspec, 'templates', templates_2func,
'inputspec.templates')
# gm_mask_templates
indnet.connect(segments_2func,
('outputspec.segments_2func_files', get_second_item),
gm_mask_templates, 'in_file')
indnet.connect(templates_2func, 'outputspec.templates_2func_files',
gm_mask_templates, 'in_file2')
# func_brainmask
indnet.connect(func_realignsmooth, 'outputspec.mean', func_brainmask,
'in_file')
# func_melodic
if melodic_seed != None:
indnet.connect(func_realignsmooth,
('outputspec.smoothed_files', get_first_item),
func_melodic, 'in_files')
indnet.connect(func_brainmask, 'mask_file', func_melodic, 'mask')
# func_aroma
indnet.connect(func_realignsmooth,
('outputspec.smoothed_files', get_first_item), func_aroma,
'in_file')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', func_aroma,
'mat_file')
indnet.connect(func_2mni, 'outputspec.anat2target_transform', func_aroma,
'fnirt_warp_file')
indnet.connect(func_realignsmooth,
('outputspec.motion_parameters', get_first_item),
func_aroma, 'motion_parameters')
indnet.connect(func_brainmask, 'mask_file', func_aroma, 'mask')
if melodic_seed != None:
indnet.connect(func_melodic, 'out_dir', func_aroma, 'melodic_dir')
# func_highpass
if aggr_aroma:
indnet.connect(func_aroma, 'aggr_denoised_file', func_highpass,
'inputspec.in_file')
else:
indnet.connect(func_aroma, 'nonaggr_denoised_file', func_highpass,
'inputspec.in_file')
# csf_meansignal
indnet.connect(segments_2func,
('outputspec.segments_2func_files', get_first_item),
csf_meansignal, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file', csf_meansignal,
'in_file')
# wm_meansignal
indnet.connect(segments_2func,
('outputspec.segments_2func_files', get_third_item),
wm_meansignal, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file', wm_meansignal,
'in_file')
# nonbrain_meansignal
indnet.connect(inputspec, 'func_file', nonbrain_meansignal,
'inputspec.func_file')
# firsteigenvariates
indnet.connect(gm_mask_templates, 'out_file', firsteigenvariates, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file',
firsteigenvariates, 'in_file')
# regressors
indnet.connect(firsteigenvariates, 'out_file', regressors, 'in1')
indnet.connect(wm_meansignal, 'out_file', regressors, 'in2')
indnet.connect(csf_meansignal, 'out_file', regressors, 'in3')
indnet.connect(nonbrain_meansignal, 'outputspec.nonbrain_regressor',
regressors, 'in4')
# ztransform
indnet.connect(regressors, 'out', ztransform, 'in_file')
# designmatrix
indnet.connect(ztransform, 'out_file', designmatrix, 'in_files')
# contrasts
indnet.connect(inputspec, ('networks', get_components), contrasts,
'in_list')
indnet.connect(designmatrix, 'out_file', contrasts, 'design')
# glm
indnet.connect(designmatrix, 'out_file', glm, 'design')
indnet.connect(contrasts, 'out_file', glm, 'contrasts')
indnet.connect(func_brainmask, 'mask_file', glm, 'mask')
indnet.connect(func_highpass, 'outputspec.filtered_file', glm, 'in_file')
# zmaps
indnet.connect(glm, 'out_z', zmaps, 'in_file')
# smm
indnet.connect(zmaps, 'out_files', smm, 'spatial_data_file')
indnet.connect(func_brainmask, 'mask_file', smm, 'mask')
# actmaps_2anat
indnet.connect(smm, 'activation_p_map', actmaps_2anat, 'in_file')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', actmaps_2anat,
'in_matrix_file')
indnet.connect(anat_bet, 'out_file', actmaps_2anat, 'reference')
# actmaps_2mni
indnet.connect(smm, 'activation_p_map', actmaps_2mni, 'in_file')
indnet.connect(templates_2func, 'outputspec.func_2mni_warp', actmaps_2mni,
'field_file')
# network_masks_func
indnet.connect(smm, 'activation_p_map', network_masks_func,
'inputspec.actmaps')
indnet.connect(inputspec, 'networks', network_masks_func,
'inputspec.networks')
# network_masks_anat
indnet.connect(actmaps_2anat, 'out_file', network_masks_anat,
'inputspec.actmaps')
indnet.connect(inputspec, 'networks', network_masks_anat,
'inputspec.networks')
# network_masks_mni
indnet.connect(actmaps_2mni, 'out_file', network_masks_mni,
'inputspec.actmaps')
indnet.connect(inputspec, 'networks', network_masks_mni,
'inputspec.networks')
# output node
indnet.connect(network_masks_func, 'outputspec.main_masks', outputspec,
'network_masks_func_main')
indnet.connect(network_masks_func, 'outputspec.exclusive_masks',
outputspec, 'network_masks_func_exclusive')
indnet.connect(network_masks_anat, 'outputspec.main_masks', outputspec,
'network_masks_anat_main')
indnet.connect(network_masks_anat, 'outputspec.exclusive_masks',
outputspec, 'network_masks_anat_exclusive')
indnet.connect(network_masks_mni, 'outputspec.main_masks', outputspec,
'network_masks_mni_main')
indnet.connect(network_masks_mni, 'outputspec.exclusive_masks', outputspec,
'network_masks_mni_exclusive')
indnet.connect(func_highpass, 'outputspec.filtered_file', outputspec,
'preprocessed_func_file')
indnet.connect(anat_segmentation, 'restored_image', outputspec,
'preprocessed_anat_file')
indnet.connect(func_realignsmooth,
('outputspec.motion_parameters', get_first_item),
outputspec, 'motion_parameters')
indnet.connect(func_2mni, 'outputspec.func2anat_transform', outputspec,
'func2anat_transform')
indnet.connect(func_2mni, 'outputspec.anat2target_transform', outputspec,
'anat2mni_transform')
return indnet
def create_nonlinear_register(name='nonlinear_register'):
"""
Performs non-linear registration of an input file to a reference file.
Parameters
----------
name : string, optional
Name of the workflow.
Returns
-------
nonlinear_register : nipype.pipeline.engine.Workflow
Notes
-----
Workflow Inputs::
inputspec.input_brain : string (nifti file)
File of brain to be normalized (registered)
inputspec.input_skull : string (nifti file)
File of input brain with skull
inputspec.reference_brain : string (nifti file)
Target brain file to normalize to
inputspec.reference_skull : string (nifti file)
Target brain with skull to normalize to
inputspec.fnirt_config : string (fsl fnirt config file)
Configuration file containing parameters that can be specified in fnirt
Workflow Outputs::
outputspec.output_brain : string (nifti file)
Normalizion of input brain file
outputspec.linear_xfm : string (.mat file)
Affine matrix of linear transformation of brain file
outputspec.invlinear_xfm : string
Inverse of affine matrix of linear transformation of brain file
outputspec.nonlinear_xfm : string
Nonlinear field coefficients file of nonlinear transformation
Registration Procedure:
1. Perform a linear registration to get affine transformation matrix.
2. Perform a nonlinear registration on an input file to the reference file utilizing affine
transformation from the previous step as a starting point.
3. Invert the affine transformation to provide the user a transformation (affine only) from the
space of the reference file to the input file.
Workflow Graph:
.. image:: ../images/nonlinear_register.dot.png
:width: 500
Detailed Workflow Graph:
.. image:: ../images/nonlinear_register_detailed.dot.png
:width: 500
"""
nonlinear_register = pe.Workflow(name=name)
inputspec = pe.Node(util.IdentityInterface(fields=[
'input_brain', 'input_skull', 'reference_brain', 'reference_skull',
'fnirt_config'
]),
name='inputspec')
outputspec = pe.Node(util.IdentityInterface(fields=[
'output_brain', 'linear_xfm', 'invlinear_xfm', 'nonlinear_xfm'
]),
name='outputspec')
linear_reg = pe.Node(interface=fsl.FLIRT(), name='linear_reg_0')
linear_reg.inputs.cost = 'corratio'
nonlinear_reg = pe.Node(interface=fsl.FNIRT(), name='nonlinear_reg_1')
nonlinear_reg.inputs.fieldcoeff_file = True
nonlinear_reg.inputs.jacobian_file = True
brain_warp = pe.Node(interface=fsl.ApplyWarp(), name='brain_warp')
inv_flirt_xfm = pe.Node(interface=fsl.utils.ConvertXFM(),
name='inv_linear_reg0_xfm')
inv_flirt_xfm.inputs.invert_xfm = True
nonlinear_register.connect(inputspec, 'input_brain', linear_reg, 'in_file')
nonlinear_register.connect(inputspec, 'reference_brain', linear_reg,
'reference')
nonlinear_register.connect(inputspec, 'input_skull', nonlinear_reg,
'in_file')
nonlinear_register.connect(inputspec, 'reference_skull', nonlinear_reg,
'ref_file')
# FNIRT parameters are specified by FSL config file
# ${FSLDIR}/etc/flirtsch/TI_2_MNI152_2mm.cnf (or user-specified)
nonlinear_register.connect(inputspec, 'fnirt_config', nonlinear_reg,
'config_file')
nonlinear_register.connect(linear_reg, 'out_matrix_file', nonlinear_reg,
'affine_file')
nonlinear_register.connect(nonlinear_reg, 'fieldcoeff_file', outputspec,
'nonlinear_xfm')
nonlinear_register.connect(inputspec, 'input_brain', brain_warp, 'in_file')
nonlinear_register.connect(nonlinear_reg, 'fieldcoeff_file', brain_warp,
'field_file')
nonlinear_register.connect(inputspec, 'reference_brain', brain_warp,
'ref_file')
nonlinear_register.connect(brain_warp, 'out_file', outputspec,
'output_brain')
nonlinear_register.connect(linear_reg, 'out_matrix_file', inv_flirt_xfm,
'in_file')
nonlinear_register.connect(inv_flirt_xfm, 'out_file', outputspec,
'invlinear_xfm')
nonlinear_register.connect(linear_reg, 'out_matrix_file', outputspec,
'linear_xfm')
return nonlinear_register
def create_register_func_to_mni(name='register_func_to_mni'):
"""
Registers a functional scan in native space to MNI standard space. This is meant to be used
after create_nonlinear_register() has been run and relies on some of it's outputs.
Parameters
----------
name : string, optional
Name of the workflow.
Returns
-------
register_func_to_mni : nipype.pipeline.engine.Workflow
Notes
-----
Workflow Inputs::
inputspec.func : string (nifti file)
Input functional scan to be registered to MNI space
inputspec.mni : string (nifti file)
Reference MNI file
inputspec.anat : string (nifti file)
Corresponding anatomical scan of subject
inputspec.interp : string
Type of interpolation to use ('trilinear' or 'nearestneighbour' or 'sinc')
inputspec.anat_to_mni_nonlinear_xfm : string (warp file)
Corresponding anatomical native space to MNI warp file
inputspec.anat_to_mni_linear_xfm : string (mat file)
Corresponding anatomical native space to MNI mat file
Workflow Outputs::
outputspec.func_to_anat_linear_xfm : string (mat file)
Affine transformation from functional to anatomical native space
outputspec.func_to_mni_linear_xfm : string (mat file)
Affine transformation from functional to MNI space
outputspec.mni_to_func_linear_xfm : string (mat file)
Affine transformation from MNI to functional space
outputspec.mni_func : string (nifti file)
Functional scan registered to MNI standard space
Workflow Graph:
.. image:: ../images/register_func_to_mni.dot.png
:width: 500
Detailed Workflow Graph:
.. image:: ../images/register_func_to_mni_detailed.dot.png
:width: 500
"""
register_func_to_mni = pe.Workflow(name=name)
inputspec = pe.Node(util.IdentityInterface(fields=[
'func', 'mni', 'anat', 'interp', 'anat_to_mni_nonlinear_xfm',
'anat_to_mni_linear_xfm'
]),
name='inputspec')
outputspec = pe.Node(util.IdentityInterface(fields=[
'func_to_anat_linear_xfm', 'func_to_mni_linear_xfm',
'mni_to_func_linear_xfm', 'mni_func'
]),
name='outputspec')
linear_reg = pe.Node(interface=fsl.FLIRT(), name='linear_func_to_anat')
linear_reg.inputs.cost = 'corratio'
linear_reg.inputs.dof = 6
mni_warp = pe.Node(interface=fsl.ApplyWarp(), name='mni_warp')
mni_affine = pe.Node(interface=fsl.ConvertXFM(), name='mni_affine')
mni_affine.inputs.concat_xfm = True
register_func_to_mni.connect(linear_reg, 'out_matrix_file', mni_affine,
'in_file2')
register_func_to_mni.connect(inputspec, 'anat_to_mni_linear_xfm',
mni_affine, 'in_file')
register_func_to_mni.connect(mni_affine, 'out_file', outputspec,
'func_to_mni_linear_xfm')
inv_mni_affine = pe.Node(interface=fsl.ConvertXFM(), name='inv_mni_affine')
inv_mni_affine.inputs.invert_xfm = True
register_func_to_mni.connect(mni_affine, 'out_file', inv_mni_affine,
'in_file')
register_func_to_mni.connect(inv_mni_affine, 'out_file', outputspec,
'mni_to_func_linear_xfm')
register_func_to_mni.connect(inputspec, 'func', linear_reg, 'in_file')
register_func_to_mni.connect(inputspec, 'anat', linear_reg, 'reference')
register_func_to_mni.connect(inputspec, 'interp', linear_reg, 'interp')
register_func_to_mni.connect(inputspec, 'func', mni_warp, 'in_file')
register_func_to_mni.connect(inputspec, 'mni', mni_warp, 'ref_file')
register_func_to_mni.connect(inputspec, 'anat_to_mni_nonlinear_xfm',
mni_warp, 'field_file')
register_func_to_mni.connect(linear_reg, 'out_matrix_file', mni_warp,
'premat')
register_func_to_mni.connect(linear_reg, 'out_matrix_file', outputspec,
'func_to_anat_linear_xfm')
register_func_to_mni.connect(mni_warp, 'out_file', outputspec, 'mni_func')
return register_func_to_mni
def create_vmhc(use_ants, name='vmhc_workflow', ants_threads=1):
"""
Compute the map of brain functional homotopy, the high degree of synchrony in spontaneous activity between geometrically corresponding interhemispheric (i.e., homotopic) regions.
Parameters
----------
None
Returns
-------
vmhc_workflow : workflow
Voxel Mirrored Homotopic Connectivity Analysis Workflow
Notes
-----
`Source <https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/vmhc/vmhc.py>`_
Workflow Inputs::
inputspec.brain : string (existing nifti file)
Anatomical image(without skull)
inputspec.symmetric_brain : string (existing nifti file)
MNI152_T1_2mm_symmetric_brain.nii.gz
inputspec.rest_res_filt : string (existing nifti file)
Band passed Image with nuisance signal regressed out(and optionally scrubbed). Recommended bandpass filter (0.001,0.1) )
inputspec.reorient : string (existing nifti file)
RPI oriented anatomical data
inputspec.example_func2highres_mat : string (existing affine transformation .mat file)
Specifies an affine transform that should be applied to the example_func before non linear warping
inputspec.standard_for_func: string (existing nifti file)
MNI152_T1_standard_resolution_brain.nii.gz
inputspec.symmetric_skull : string (existing nifti file)
MNI152_T1_2mm_symmetric.nii.gz
inputspec.twomm_brain_mask_dil : string (existing nifti file)
MNI152_T1_2mm_brain_mask_symmetric_dil.nii.gz
inputspec.config_file_twomm_symmetric : string (existing .cnf file)
T1_2_MNI152_2mm_symmetric.cnf
inputspec.rest_mask : string (existing nifti file)
A mask functional volume(derived by dilation from motion corrected functional volume)
fwhm_input.fwhm : list (float)
For spatial smoothing the Z-transformed correlations in MNI space.
Generally the value of this parameter is 1.5 or 2 times the voxel size of the input Image.
inputspec.mean_functional : string (existing nifti file)
The mean functional image for use in the func-to-anat registration matrix conversion
to ITK (ANTS) format, if the user selects to use ANTS.
Workflow Outputs::
outputspec.highres2symmstandard : string (nifti file)
Linear registration of T1 image to symmetric standard image
outputspec.highres2symmstandard_mat : string (affine transformation .mat file)
An affine transformation .mat file from linear registration and used in non linear registration
outputspec.highres2symmstandard_warp : string (nifti file)
warp file from Non Linear registration of T1 to symmetrical standard brain
outputspec.fnirt_highres2symmstandard : string (nifti file)
Non Linear registration of T1 to symmetrical standard brain
outputspec.highres2symmstandard_jac : string (nifti file)
jacobian determinant image from Non Linear registration of T1 to symmetrical standard brain
outputspec.rest_res_2symmstandard : string (nifti file)
nonlinear registration (func to standard) image
outputspec.VMHC_FWHM_img : string (nifti file)
pearson correlation between res2standard and flipped res2standard
outputspec.VMHC_Z_FWHM_img : string (nifti file)
Fisher Z transform map
outputspec.VMHC_Z_stat_FWHM_img : string (nifti file)
Z statistic map
Order of commands:
- Perform linear registration of Anatomical brain in T1 space to symmetric standard space. For details see `flirt <http://www.fmrib.ox.ac.uk/fsl/flirt/index.html>`_::
flirt
-ref MNI152_T1_2mm_symmetric_brain.nii.gz
-in mprage_brain.nii.gz
-out highres2symmstandard.nii.gz
-omat highres2symmstandard.mat
-cost corratio
-searchcost corratio
-dof 12
-interp trilinear
- Perform nonlinear registration (higres to standard) to symmetric standard brain. For details see `fnirt <http://fsl.fmrib.ox.ac.uk/fsl/fnirt/>`_::
fnirt
--in=head.nii.gz
--aff=highres2symmstandard.mat
--cout=highres2symmstandard_warp.nii.gz
--iout=fnirt_highres2symmstandard.nii.gz
--jout=highres2symmstandard_jac.nii.gz
--config=T1_2_MNI152_2mm_symmetric.cnf
--ref=MNI152_T1_2mm_symmetric.nii.gz
--refmask=MNI152_T1_2mm_brain_mask_symmetric_dil.nii.gz
--warpres=10,10,10
- Perform spatial smoothing on the input functional image(inputspec.rest_res_filt). For details see `PrinciplesSmoothing <http://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesSmoothing>`_ `fslmaths <http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro/index.htm>`_::
fslmaths rest_res_filt.nii.gz
-kernel gauss FWHM/ sqrt(8-ln(2))
-fmean -mas rest_mask.nii.gz
rest_res_filt_FWHM.nii.gz
- Apply nonlinear registration (func to standard). For details see `applywarp <http://www.fmrib.ox.ac.uk/fsl/fnirt/warp_utils.html#applywarp>`_::
applywarp
--ref=MNI152_T1_2mm_symmetric.nii.gz
--in=rest_res_filt_FWHM.nii.gz
--out=rest_res_2symmstandard.nii.gz
--warp=highres2symmstandard_warp.nii.gz
--premat=example_func2highres.mat
- Copy and L/R swap the output of applywarp command (rest_res_2symmstandard.nii.gz). For details see `fslswapdim <http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/avwutils/index.html>`_::
fslswapdim
rest_res_2symmstandard.nii.gz
-x y z
tmp_LRflipped.nii.gz
- Calculate pearson correlation between rest_res_2symmstandard.nii.gz and flipped rest_res_2symmstandard.nii.gz(tmp_LRflipped.nii.gz). For details see `3dTcorrelate <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcorrelate.html>`_::
3dTcorrelate
-pearson
-polort -1
-prefix VMHC_FWHM.nii.gz
rest_res_2symmstandard.nii.gz
tmp_LRflipped.nii.gz
- Fisher Z Transform the correlation. For details see `3dcalc <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dcalc.html>`_::
3dcalc
-a VMHC_FWHM.nii.gz
-expr 'log((a+1)/(1-a))/2'
-prefix VMHC_FWHM_Z.nii.gz
- Calculate the number of volumes(nvols) in flipped rest_res_2symmstandard.nii.gz(tmp_LRflipped.nii.gz) ::
-Use Nibabel to do this
- Compute the Z statistic map ::
3dcalc
-a VMHC_FWHM_Z.nii.gz
-expr 'a*sqrt('${nvols}'-3)'
-prefix VMHC_FWHM_Z_stat.nii.gz
Workflow:
.. image:: ../images/vmhc_graph.dot.png
:width: 500
Workflow Detailed:
.. image:: ../images/vmhc_detailed_graph.dot.png
:width: 500
References
----------
.. [1] Zuo, X.-N., Kelly, C., Di Martino, A., Mennes, M., Margulies, D. S., Bangaru, S., Grzadzinski, R., et al. (2010). Growing together and growing apart: regional and sex differences in the lifespan developmental trajectories of functional homotopy. The Journal of neuroscience : the official journal of the Society for Neuroscience, 30(45), 15034-43. doi:10.1523/JNEUROSCI.2612-10.2010
Examples
--------
>>> vmhc_w = create_vmhc()
>>> vmhc_w.inputs.inputspec.symmetric_brain = 'MNI152_T1_2mm_symmetric_brain.nii.gz'
>>> vmhc_w.inputs.inputspec.symmetric_skull = 'MNI152_T1_2mm_symmetric.nii.gz'
>>> vmhc_w.inputs.inputspec.twomm_brain_mask_dil = 'MNI152_T1_2mm_brain_mask_symmetric_dil.nii.gz'
>>> vmhc_w.inputs.inputspec.config_file_twomm = 'T1_2_MNI152_2mm_symmetric.cnf'
>>> vmhc_w.inputs.inputspec.standard_for_func= 'MNI152_T1_2mm.nii.gz'
>>> vmhc_w.inputs.fwhm_input.fwhm = [4.5, 6]
>>> vmhc_w.get_node('fwhm_input').iterables = ('fwhm', [4.5, 6])
>>> vmhc_w.inputs.inputspec.rest_res = os.path.abspath('/home/data/Projects/Pipelines_testing/Dickstein/subjects/s1001/func/original/rest_res_filt.nii.gz')
>>> vmhc_w.inputs.inputspec.reorient = os.path.abspath('/home/data/Projects/Pipelines_testing/Dickstein/subjects/s1001/anat/mprage_RPI.nii.gz')
>>> vmhc_w.inputs.inputspec.brain = os.path.abspath('/home/data/Projects/Pipelines_testing/Dickstein/subjects/s1001/anat/mprage_brain.nii.gz')
>>> vmhc_w.inputs.inputspec.example_func2highres_mat = os.path.abspath('/home/data/Projects/Pipelines_testing/Dickstein/subjects/s1001/func/original/reg/example_func2highres.mat')
>>> vmhc_w.inputs.inputspec.rest_mask = os.path.abspath('/home/data/Projects/Pipelines_testing/Dickstein/subjects/s1001/func/original/rest_mask.nii.gz')
>>> vmhc_w.run() # doctest: +SKIP
"""
vmhc = pe.Workflow(name=name)
inputNode = pe.Node(util.IdentityInterface(fields=[
'rest_res', 'example_func2highres_mat', 'rest_mask',
'standard_for_func', 'mean_functional', 'brain',
'fnirt_nonlinear_warp', 'ants_symm_initial_xfm', 'ants_symm_rigid_xfm',
'ants_symm_affine_xfm', 'ants_symm_warp_field'
]),
name='inputspec')
outputNode = pe.Node(util.IdentityInterface(fields=[
'rest_res_2symmstandard', 'VMHC_FWHM_img', 'VMHC_Z_FWHM_img',
'VMHC_Z_stat_FWHM_img'
]),
name='outputspec')
inputnode_fwhm = pe.Node(util.IdentityInterface(fields=['fwhm']),
name='fwhm_input')
if use_ants == False:
# Apply nonlinear registration (func to standard)
nonlinear_func_to_standard = pe.Node(interface=fsl.ApplyWarp(),
name='nonlinear_func_to_standard')
elif use_ants == True:
# ANTS warp image etc.
fsl_to_itk_vmhc = create_wf_c3d_fsl_to_itk(0, name='fsl_to_itk_vmhc')
collect_transforms_vmhc = create_wf_collect_transforms(
0, name='collect_transforms_vmhc')
apply_ants_xfm_vmhc = create_wf_apply_ants_warp(
0, name='apply_ants_xfm_vmhc', ants_threads=ants_threads)
# this has to be 3 instead of default 0 because it is a 4D file
apply_ants_xfm_vmhc.inputs.inputspec.input_image_type = 3
# copy and L/R swap file
copy_and_L_R_swap = pe.Node(interface=fsl.SwapDimensions(),
name='copy_and_L_R_swap')
copy_and_L_R_swap.inputs.new_dims = ('-x', 'y', 'z')
# calculate vmhc
pearson_correlation = pe.Node(interface=preprocess.TCorrelate(),
name='pearson_correlation')
pearson_correlation.inputs.pearson = True
pearson_correlation.inputs.polort = -1
pearson_correlation.inputs.outputtype = 'NIFTI_GZ'
try:
z_trans = pe.Node(interface=preprocess.Calc(), name='z_trans')
z_stat = pe.Node(interface=preprocess.Calc(), name='z_stat')
except AttributeError:
from nipype.interfaces.afni import utils as afni_utils
z_trans = pe.Node(interface=afni_utils.Calc(), name='z_trans')
z_stat = pe.Node(interface=afni_utils.Calc(), name='z_stat')
z_trans.inputs.expr = 'log((1+a)/(1-a))/2'
z_trans.inputs.outputtype = 'NIFTI_GZ'
z_stat.inputs.outputtype = 'NIFTI_GZ'
NVOLS = pe.Node(util.Function(input_names=['in_files'],
output_names=['nvols'],
function=get_img_nvols),
name='NVOLS')
generateEXP = pe.Node(util.Function(input_names=['nvols'],
output_names=['expr'],
function=get_operand_expression),
name='generateEXP')
smooth = pe.Node(interface=fsl.MultiImageMaths(), name='smooth')
if use_ants == False:
vmhc.connect(inputNode, 'rest_res', smooth, 'in_file')
vmhc.connect(inputnode_fwhm, ('fwhm', set_gauss), smooth, 'op_string')
vmhc.connect(inputNode, 'rest_mask', smooth, 'operand_files')
vmhc.connect(smooth, 'out_file', nonlinear_func_to_standard, 'in_file')
vmhc.connect(inputNode, 'standard_for_func',
nonlinear_func_to_standard, 'ref_file')
vmhc.connect(inputNode, 'fnirt_nonlinear_warp',
nonlinear_func_to_standard, 'field_file')
## func->anat matrix (bbreg)
vmhc.connect(inputNode, 'example_func2highres_mat',
nonlinear_func_to_standard, 'premat')
vmhc.connect(nonlinear_func_to_standard, 'out_file', copy_and_L_R_swap,
'in_file')
vmhc.connect(nonlinear_func_to_standard, 'out_file',
pearson_correlation, 'xset')
elif use_ants == True:
# connections for ANTS stuff
# functional apply warp stuff
vmhc.connect(inputNode, 'rest_res', smooth, 'in_file')
vmhc.connect(inputnode_fwhm, ('fwhm', set_gauss), smooth, 'op_string')
vmhc.connect(inputNode, 'rest_mask', smooth, 'operand_files')
vmhc.connect(smooth, 'out_file', apply_ants_xfm_vmhc,
'inputspec.input_image')
vmhc.connect(inputNode, 'ants_symm_initial_xfm',
collect_transforms_vmhc, 'inputspec.linear_initial')
vmhc.connect(inputNode, 'ants_symm_rigid_xfm', collect_transforms_vmhc,
'inputspec.linear_rigid')
vmhc.connect(inputNode, 'ants_symm_affine_xfm',
collect_transforms_vmhc, 'inputspec.linear_affine')
vmhc.connect(inputNode, 'ants_symm_warp_field',
collect_transforms_vmhc, 'inputspec.warp_file')
# func->anat matrix (bbreg)
vmhc.connect(inputNode, 'example_func2highres_mat', fsl_to_itk_vmhc,
'inputspec.affine_file')
vmhc.connect(inputNode, 'brain', fsl_to_itk_vmhc,
'inputspec.reference_file')
vmhc.connect(inputNode, 'mean_functional', fsl_to_itk_vmhc,
'inputspec.source_file')
vmhc.connect(fsl_to_itk_vmhc, 'outputspec.itk_transform',
collect_transforms_vmhc, 'inputspec.fsl_to_itk_affine')
vmhc.connect(inputNode, 'standard_for_func', apply_ants_xfm_vmhc,
'inputspec.reference_image')
vmhc.connect(collect_transforms_vmhc,
'outputspec.transformation_series', apply_ants_xfm_vmhc,
'inputspec.transforms')
vmhc.connect(apply_ants_xfm_vmhc, 'outputspec.output_image',
copy_and_L_R_swap, 'in_file')
vmhc.connect(apply_ants_xfm_vmhc, 'outputspec.output_image',
pearson_correlation, 'xset')
vmhc.connect(copy_and_L_R_swap, 'out_file', pearson_correlation, 'yset')
vmhc.connect(pearson_correlation, 'out_file', z_trans, 'in_file_a')
vmhc.connect(copy_and_L_R_swap, 'out_file', NVOLS, 'in_files')
vmhc.connect(NVOLS, 'nvols', generateEXP, 'nvols')
vmhc.connect(z_trans, 'out_file', z_stat, 'in_file_a')
vmhc.connect(generateEXP, 'expr', z_stat, 'expr')
if use_ants == False:
vmhc.connect(nonlinear_func_to_standard, 'out_file', outputNode,
'rest_res_2symmstandard')
elif use_ants == True:
# ANTS warp outputs to outputnode
vmhc.connect(apply_ants_xfm_vmhc, 'outputspec.output_image',
outputNode, 'rest_res_2symmstandard')
vmhc.connect(pearson_correlation, 'out_file', outputNode, 'VMHC_FWHM_img')
vmhc.connect(z_trans, 'out_file', outputNode, 'VMHC_Z_FWHM_img')
vmhc.connect(z_stat, 'out_file', outputNode, 'VMHC_Z_stat_FWHM_img')
return vmhc
def define_preproc_workflow(info, subjects, sessions, qc=True):
# --- Workflow parameterization and data input
scan_info = info.scan_info
experiment = info.experiment_name
iterables = generate_iterables(scan_info, experiment, subjects, sessions)
subject_iterables, session_iterables, run_iterables = iterables
subject_iterables = subjects
subject_source = Node(IdentityInterface(["subject"]),
name="subject_source",
iterables=("subject", subject_iterables))
session_source = Node(IdentityInterface(["subject", "session"]),
name="session_source",
itersource=("subject_source", "subject"),
iterables=("session", session_iterables))
run_source = Node(IdentityInterface(["subject", "session", "run"]),
name="run_source",
itersource=("session_source", "session"),
iterables=("run", run_iterables))
session_input = Node(SessionInput(data_dir=info.data_dir,
proc_dir=info.proc_dir,
fm_template=info.fm_template,
phase_encoding=info.phase_encoding),
"session_input")
run_input = Node(RunInput(experiment=experiment,
data_dir=info.data_dir,
proc_dir=info.proc_dir,
sb_template=info.sb_template,
ts_template=info.ts_template,
crop_frames=info.crop_frames),
name="run_input")
# --- Warpfield estimation using topup
# Distortion warpfield estimation
# TODO figure out how to parameterize for testing
# topup_config = op.realpath(op.join(__file__, "../../../topup_fast.cnf"))
topup_config = "b02b0.cnf"
estimate_distortions = Node(fsl.TOPUP(config=topup_config),
"estimate_distortions")
# Post-process the TOPUP outputs
finalize_unwarping = Node(FinalizeUnwarping(), "finalize_unwarping")
# --- Registration of SE-EPI (without distortions) to Freesurfer anatomy
fm2anat = Node(fs.BBRegister(init="fsl",
contrast_type="t2",
registered_file=True,
out_fsl_file="sess2anat.mat",
out_reg_file="sess2anat.dat"),
"fm2anat")
fm2anat_qc = Node(AnatRegReport(data_dir=info.data_dir), "fm2anat_qc")
# --- Registration of SBRef to SE-EPI (with distortions)
sb2fm = Node(fsl.FLIRT(dof=6, interp="spline"), "sb2fm")
sb2fm_qc = Node(CoregGIF(out_file="coreg.gif"), "sb2fm_qc")
# --- Motion correction of time series to SBRef (with distortions)
ts2sb = Node(fsl.MCFLIRT(save_mats=True, save_plots=True),
"ts2sb")
ts2sb_qc = Node(RealignmentReport(), "ts2sb_qc")
# --- Combined motion correction, unwarping, and template registration
# Combine pre-and post-warp linear transforms
combine_premats = MapNode(fsl.ConvertXFM(concat_xfm=True),
"in_file", "combine_premats")
combine_postmats = Node(fsl.ConvertXFM(concat_xfm=True),
"combine_postmats")
# Transform Jacobian images into the template space
transform_jacobian = Node(fsl.ApplyWarp(relwarp=True),
"transform_jacobian")
# Apply rigid transforms and nonlinear warpfield to time series frames
restore_timeseries = MapNode(fsl.ApplyWarp(interp="spline", relwarp=True),
["in_file", "premat"],
"restore_timeseries")
# Apply rigid transforms and nonlinear warpfield to template frames
restore_template = MapNode(fsl.ApplyWarp(interp="spline", relwarp=True),
["in_file", "premat", "field_file"],
"restore_template")
# Perform final preprocessing operations on timeseries
finalize_timeseries = Node(FinalizeTimeseries(experiment=experiment),
"finalize_timeseries")
# Perform final preprocessing operations on template
finalize_template = JoinNode(FinalizeTemplate(experiment=experiment),
name="finalize_template",
joinsource="run_source",
joinfield=["mean_files", "tsnr_files",
"mask_files", "noise_files"])
# --- Workflow ouptut
save_info = Node(SaveInfo(info_dict=info.trait_get()), "save_info")
template_output = Node(DataSink(base_directory=info.proc_dir,
parameterization=False),
"template_output")
timeseries_output = Node(DataSink(base_directory=info.proc_dir,
parameterization=False),
"timeseries_output")
# === Assemble pipeline
cache_base = op.join(info.cache_dir, info.experiment_name)
workflow = Workflow(name="preproc", base_dir=cache_base)
# Connect processing nodes
processing_edges = [
(subject_source, session_source,
[("subject", "subject")]),
(subject_source, run_source,
[("subject", "subject")]),
(session_source, run_source,
[("session", "session")]),
(session_source, session_input,
[("session", "session")]),
(run_source, run_input,
[("run", "run")]),
# Phase-encode distortion estimation
(session_input, estimate_distortions,
[("fm_file", "in_file"),
("phase_encoding", "encoding_direction"),
("readout_times", "readout_times")]),
(session_input, finalize_unwarping,
[("fm_file", "raw_file"),
("phase_encoding", "phase_encoding")]),
(estimate_distortions, finalize_unwarping,
[("out_corrected", "corrected_file"),
("out_warps", "warp_files"),
("out_jacs", "jacobian_files")]),
# Registration of corrected SE-EPI to anatomy
(session_input, fm2anat,
[("subject", "subject_id")]),
(finalize_unwarping, fm2anat,
[("corrected_file", "source_file")]),
# Registration of each frame to SBRef image
(run_input, ts2sb,
[("ts_file", "in_file"),
("sb_file", "ref_file")]),
(ts2sb, finalize_timeseries,
[("par_file", "mc_file")]),
# Registration of SBRef volume to SE-EPI fieldmap
(run_input, sb2fm,
[("sb_file", "in_file")]),
(finalize_unwarping, sb2fm,
[("raw_file", "reference"),
("mask_file", "ref_weight")]),
# Single-interpolation spatial realignment and unwarping
(ts2sb, combine_premats,
[("mat_file", "in_file")]),
(sb2fm, combine_premats,
[("out_matrix_file", "in_file2")]),
(fm2anat, combine_postmats,
[("out_fsl_file", "in_file")]),
(session_input, combine_postmats,
[("reg_file", "in_file2")]),
(run_input, transform_jacobian,
[("anat_file", "ref_file")]),
(finalize_unwarping, transform_jacobian,
[("jacobian_file", "in_file")]),
(combine_postmats, transform_jacobian,
[("out_file", "premat")]),
(run_input, restore_timeseries,
[("ts_frames", "in_file")]),
(run_input, restore_timeseries,
[("anat_file", "ref_file")]),
(combine_premats, restore_timeseries,
[("out_file", "premat")]),
(finalize_unwarping, restore_timeseries,
[("warp_file", "field_file")]),
(combine_postmats, restore_timeseries,
[("out_file", "postmat")]),
(run_input, finalize_timeseries,
[("run_tuple", "run_tuple"),
("anat_file", "anat_file"),
("seg_file", "seg_file"),
("mask_file", "mask_file")]),
(transform_jacobian, finalize_timeseries,
[("out_file", "jacobian_file")]),
(restore_timeseries, finalize_timeseries,
[("out_file", "in_files")]),
(session_input, restore_template,
[("fm_frames", "in_file"),
("anat_file", "ref_file")]),
(estimate_distortions, restore_template,
[("out_mats", "premat"),
("out_warps", "field_file")]),
(combine_postmats, restore_template,
[("out_file", "postmat")]),
(session_input, finalize_template,
[("session_tuple", "session_tuple"),
("seg_file", "seg_file"),
("anat_file", "anat_file")]),
(transform_jacobian, finalize_template,
[("out_file", "jacobian_file")]),
(restore_template, finalize_template,
[("out_file", "in_files")]),
(finalize_timeseries, finalize_template,
[("mean_file", "mean_files"),
("tsnr_file", "tsnr_files"),
("mask_file", "mask_files"),
("noise_file", "noise_files")]),
# --- Persistent data storage
# Ouputs associated with each scanner run
(finalize_timeseries, timeseries_output,
[("output_path", "container"),
("out_file", "@func"),
("mean_file", "@mean"),
("mask_file", "@mask"),
("tsnr_file", "@tsnr"),
("noise_file", "@noise"),
("mc_file", "@mc")]),
# Ouputs associated with the session template
(finalize_template, template_output,
[("output_path", "container"),
("out_file", "@func"),
("mean_file", "@mean"),
("tsnr_file", "@tsnr"),
("mask_file", "@mask"),
("noise_file", "@noise")]),
]
workflow.connect(processing_edges)
# Optionally connect QC nodes
qc_edges = [
# Registration of each frame to SBRef image
(run_input, ts2sb_qc,
[("sb_file", "target_file")]),
(ts2sb, ts2sb_qc,
[("par_file", "realign_params")]),
# Registration of corrected SE-EPI to anatomy
(session_input, fm2anat_qc,
[("subject", "subject_id")]),
(fm2anat, fm2anat_qc,
[("registered_file", "in_file"),
("min_cost_file", "cost_file")]),
# Registration of SBRef volume to SE-EPI fieldmap
(sb2fm, sb2fm_qc,
[("out_file", "in_file")]),
(finalize_unwarping, sb2fm_qc,
[("raw_file", "ref_file")]),
# Ouputs associated with each scanner run
(run_source, save_info,
[("run", "parameterization")]),
(save_info, timeseries_output,
[("info_file", "qc.@info_json")]),
(run_input, timeseries_output,
[("ts_plot", "qc.@raw_gif")]),
(sb2fm_qc, timeseries_output,
[("out_file", "qc.@sb2fm_gif")]),
(ts2sb_qc, timeseries_output,
[("params_plot", "qc.@params_plot"),
("target_plot", "qc.@target_plot")]),
(finalize_timeseries, timeseries_output,
[("out_gif", "qc.@ts_gif"),
("out_png", "qc.@ts_png"),
("mask_plot", "qc.@mask_plot"),
("mean_plot", "qc.@ts_mean_plot"),
("tsnr_plot", "qc.@ts_tsnr_plot"),
("noise_plot", "qc.@noise_plot")]),
# Outputs associated with the session template
(finalize_unwarping, template_output,
[("warp_plot", "qc.@warp_png"),
("unwarp_gif", "qc.@unwarp_gif")]),
(fm2anat_qc, template_output,
[("out_file", "qc.@reg_png")]),
(finalize_template, template_output,
[("out_plot", "qc.@func_png"),
("mean_plot", "qc.@mean"),
("tsnr_plot", "qc.@tsnr"),
("mask_plot", "qc.@mask"),
("noise_plot", "qc.@noise")]),
]
if qc:
workflow.connect(qc_edges)
return workflow
masterdi = '/data/pt_neuam005/FSTIM_1_Think_preprocessed/fmriprep/sub-10/ses-01/func/' masterte = 'sub-10_ses-01_task-future_bold_space-MNI152NLin2009cAsym_preproc.nii.gz' masterfi = os.path.join(masterdi, masterte) os.chdir(myindata) # afni resample resample = afni.Resample() resample.inputs.in_file = 'mni_icbm152_t1_tal_nlin_asym_09c.nii' resample.inputs.voxel_size = (2.0, 2.0, 2.0) resample.inputs.master = masterfi resample.inputs.outputtype = 'NIFTI' resample.inputs.out_file = 'mni_icbm152_t1_tal_nlin_asym_09c_2mm.nii.gz' print(resample.cmdline) resample.run() # transforming template mask to 2mm (fsl nonlinear transform) aw = fsl.ApplyWarp() aw.inputs.in_file = 'mni_icbm152_t1_tal_nlin_asym_09c_mask.nii' aw.inputs.ref_file = 'mni_icbm152_t1_tal_nlin_asym_09c_2mm.nii.gz' aw.inputs.out_file = 'mni_icbm152_t1_tal_nlin_asym_09c_2mm_trf.nii.gz' print(aw.cmdline) aw.run() binar = fsl.maths.MathsCommand() binar.inputs.args = '-thr 0.90 -bin' binar.inputs.in_file = 'mni_icbm152_t1_tal_nlin_asym_09c_2mm_trf.nii.gz' binar.inputs.out_file = 'mni_icbm152_t1_tal_nlin_asym_09c_2mm_mask.nii.gz' print(binar.cmdline) binar.run()
def create_tbss_non_FA(name='tbss_non_FA'):
"""
A pipeline that implement tbss_non_FA in FSL
Example
-------
>>> from nipype.workflows.dmri.fsl import tbss
>>> tbss_MD = tbss.create_tbss_non_FA()
>>> tbss_MD.inputs.inputnode.file_list = []
>>> tbss_MD.inputs.inputnode.field_list = []
>>> tbss_MD.inputs.inputnode.skeleton_thresh = 0.2
>>> tbss_MD.inputs.inputnode.groupmask = './xxx'
>>> tbss_MD.inputs.inputnode.meanfa_file = './xxx'
>>> tbss_MD.inputs.inputnode.distance_map = []
Inputs::
inputnode.file_list
inputnode.field_list
inputnode.skeleton_thresh
inputnode.groupmask
inputnode.meanfa_file
inputnode.distance_map
Outputs::
outputnode.projected_nonFA_file
"""
# Define the inputnode
inputnode = pe.Node(interface=util.IdentityInterface(fields=[
'file_list', 'field_list', 'skeleton_thresh', 'groupmask',
'meanfa_file', 'distance_map'
]),
name='inputnode')
# Apply the warpfield to the non FA image
applywarp = pe.MapNode(interface=fsl.ApplyWarp(),
iterfield=['in_file', 'field_file'],
name="applywarp")
if fsl.no_fsl():
warn('NO FSL found')
else:
applywarp.inputs.ref_file = fsl.Info.standard_image(
"FMRIB58_FA_1mm.nii.gz")
# Merge the non FA files into a 4D file
merge = pe.Node(fsl.Merge(dimension="t"), name="merge")
#merged_file="all_FA.nii.gz"
maskgroup = pe.Node(fsl.ImageMaths(op_string="-mas", suffix="_masked"),
name="maskgroup")
projectfa = pe.Node(
fsl.TractSkeleton(
project_data=True,
#projected_data = 'test.nii.gz',
use_cingulum_mask=True),
name="projectfa")
tbss_non_FA = pe.Workflow(name=name)
tbss_non_FA.connect([
(inputnode, applywarp, [
('file_list', 'in_file'),
('field_list', 'field_file'),
]),
(applywarp, merge, [("out_file", "in_files")]),
(merge, maskgroup, [("merged_file", "in_file")]),
(inputnode, maskgroup, [('groupmask', 'in_file2')]),
(maskgroup, projectfa, [('out_file', 'data_file')]),
(inputnode, projectfa, [
('skeleton_thresh', 'threshold'),
("meanfa_file", "in_file"),
("distance_map", "distance_map"),
]),
])
# Define the outputnode
outputnode = pe.Node(
interface=util.IdentityInterface(fields=['projected_nonFA_file']),
name='outputnode')
tbss_non_FA.connect([
(projectfa, outputnode, [
('projected_data', 'projected_nonFA_file'),
]),
])
return tbss_non_FA
def create_qc_snr(wf_name='qc_snr'):
wf = pe.Workflow(name=wf_name)
input_node = pe.Node(util.IdentityInterface(fields=[
'functional_preprocessed', 'functional_brain_mask',
'functional_to_anat_linear_xfm', 'anatomical_brain',
'mean_functional_in_anat'
]),
name='inputspec')
output_node = pe.Node(util.IdentityInterface(fields=[
'snr_axial_image', 'snr_sagittal_image', 'snr_histogram_image',
'snr_mean'
]),
name='outputspec')
std_dev = pe.Node(afni.TStat(args='-stdev'), name='std_dev')
std_dev.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'functional_preprocessed', std_dev, 'in_file')
wf.connect(input_node, 'functional_brain_mask', std_dev, 'mask')
std_dev_anat = pe.Node(fsl.ApplyWarp(interp='trilinear'),
name='std_dev_anat')
wf.connect(input_node, 'functional_to_anat_linear_xfm', std_dev_anat,
'premat')
wf.connect(std_dev, 'out_file', std_dev_anat, 'in_file')
wf.connect(input_node, 'anatomical_brain', std_dev_anat, 'ref_file')
snr = pe.Node(afni.Calc(expr='b/a'), name='snr')
snr.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'mean_functional_in_anat', snr, 'in_file_b')
wf.connect(std_dev_anat, 'out_file', snr, 'in_file_a')
snr_val = pe.Node(Function(input_names=['measure_file'],
output_names=['snr_storefl'],
function=cal_snr_val,
as_module=True),
name='snr_val')
wf.connect(snr, 'out_file', snr_val, 'measure_file')
hist_snr = pe.Node(Function(input_names=['measure_file', 'measure'],
output_names=['hist_path'],
function=gen_histogram,
as_module=True),
name='hist_snr')
hist_snr.inputs.measure = 'snr'
wf.connect(snr, 'out_file', hist_snr, 'measure_file')
snr_drop_percent = pe.Node(Function(
input_names=['measure_file', 'percent'],
output_names=['modified_measure_file'],
function=drop_percent,
as_module=True),
name='dp_snr')
snr_drop_percent.inputs.percent = 99
wf.connect(snr, 'out_file', snr_drop_percent, 'measure_file')
montage_snr = create_montage('montage_snr', 'red_to_blue', 'snr')
wf.connect(snr_drop_percent, 'modified_measure_file', montage_snr,
'inputspec.overlay')
wf.connect(input_node, 'anatomical_brain', montage_snr,
'inputspec.underlay')
wf.connect(montage_snr, 'outputspec.axial_png', output_node,
'snr_axial_image')
wf.connect(montage_snr, 'outputspec.sagittal_png', output_node,
'snr_sagittal_image')
wf.connect(hist_snr, 'hist_path', output_node, 'snr_histogram_image')
wf.connect(snr_val, 'snr_storefl', output_node, 'snr_mean')
return wf
def create_reg_workflow(name='registration'):
"""Create a FEAT preprocessing workflow together with freesurfer
Parameters
----------
::
name : name of workflow (default: 'registration')
Inputs::
inputspec.source_files : files (filename or list of filenames to register)
inputspec.mean_image : reference image to use
inputspec.anatomical_image : anatomical image to coregister to
inputspec.target_image : registration target
Outputs::
outputspec.func2anat_transform : FLIRT transform
outputspec.anat2target_transform : FLIRT+FNIRT transform
outputspec.transformed_files : transformed files in target space
outputspec.transformed_mean : mean image in target space
Example
-------
"""
register = pe.Workflow(name=name)
inputnode = pe.Node(interface=util.IdentityInterface(fields=['source_files',
'mean_image',
'anatomical_image',
'target_image']),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(fields=['func2anat_transform',
'anat2target_transform',
'transformed_files',
'transformed_mean',
]),
name='outputspec')
"""
Estimate the tissue classes from the anatomical image. But use spm's segment
as FSL appears to be breaking.
"""
stripper = pe.Node(fsl.BET(), name='stripper')
register.connect(inputnode, 'anatomical_image', stripper, 'in_file')
fast = pe.Node(fsl.FAST(), name='fast')
register.connect(stripper, 'out_file', fast, 'in_files')
"""
Binarize the segmentation
"""
binarize = pe.Node(fsl.ImageMaths(op_string='-nan -thr 0.5 -bin'),
name='binarize')
pickindex = lambda x, i: x[i]
register.connect(fast, ('partial_volume_files', pickindex, 2),
binarize, 'in_file')
"""
Calculate rigid transform from mean image to anatomical image
"""
mean2anat = pe.Node(fsl.FLIRT(), name='mean2anat')
mean2anat.inputs.dof = 6
register.connect(inputnode, 'mean_image', mean2anat, 'in_file')
register.connect(stripper, 'out_file', mean2anat, 'reference')
"""
Now use bbr cost function to improve the transform
"""
mean2anatbbr = pe.Node(fsl.FLIRT(), name='mean2anatbbr')
mean2anatbbr.inputs.dof = 6
mean2anatbbr.inputs.cost = 'bbr'
mean2anatbbr.inputs.schedule = os.path.join(os.getenv('FSLDIR'),
'etc/flirtsch/bbr.sch')
register.connect(inputnode, 'mean_image', mean2anatbbr, 'in_file')
register.connect(binarize, 'out_file', mean2anatbbr, 'wm_seg')
register.connect(inputnode, 'anatomical_image', mean2anatbbr, 'reference')
register.connect(mean2anat, 'out_matrix_file', mean2anatbbr, 'in_matrix_file')
"""
Calculate affine transform from anatomical to target
"""
anat2target_affine = pe.Node(fsl.FLIRT(), name='anat2target_linear')
register.connect(inputnode, 'anatomical_image', anat2target_affine, 'in_file')
register.connect(inputnode, 'target_image', anat2target_affine, 'reference')
"""
Calculate nonlinear transform from anatomical to target
"""
anat2target_nonlinear = pe.Node(fsl.FNIRT(), name='anat2target_nonlinear')
anat2target_nonlinear.inputs.fieldcoeff_file=True
register.connect(anat2target_affine, 'out_matrix_file',
anat2target_nonlinear, 'affine_file')
anat2target_nonlinear.inputs.warp_resolution = (8, 8, 8)
register.connect(inputnode, 'anatomical_image', anat2target_nonlinear, 'in_file')
register.connect(inputnode, 'target_image',
anat2target_nonlinear, 'ref_file')
"""
Transform the mean image. First to anatomical and then to target
"""
warp2anat = pe.Node(fsl.ApplyWarp(interp='spline'), name='warp2anat')
register.connect(inputnode, 'mean_image', warp2anat, 'in_file')
register.connect(inputnode, 'anatomical_image', warp2anat, 'ref_file')
register.connect(mean2anatbbr, 'out_matrix_file', warp2anat, 'premat')
warpmean = warp2anat.clone(name='warpmean')
register.connect(warp2anat, 'out_file', warpmean, 'in_file')
register.connect(inputnode, 'target_image', warpmean, 'ref_file')
register.connect(anat2target_nonlinear, 'fieldcoeff_file',
warpmean, 'field_file')
"""
Transform the remaining images. First to anatomical and then to target
"""
warpall2anat = pe.MapNode(fsl.ApplyWarp(interp='spline'),
iterfield=['in_file'],
name='warpall2anat')
register.connect(inputnode, 'source_files', warpall2anat, 'in_file')
register.connect(inputnode, 'anatomical_image', warpall2anat, 'ref_file')
register.connect(mean2anatbbr, 'out_matrix_file', warpall2anat, 'premat')
warpall = warpall2anat.clone(name='warpall')
register.connect(warpall2anat, 'out_file', warpall, 'in_file')
register.connect(inputnode, 'target_image', warpall, 'ref_file')
register.connect(anat2target_nonlinear, 'fieldcoeff_file',
warpall, 'field_file')
"""
Assign all the output files
"""
register.connect(warpmean, 'out_file', outputnode, 'transformed_mean')
register.connect(warpall, 'out_file', outputnode, 'transformed_files')
register.connect(mean2anatbbr, 'out_matrix_file',
outputnode, 'func2anat_transform')
register.connect(anat2target_nonlinear, 'fieldcoeff_file',
outputnode, 'anat2target_transform')
return register
def create_fsl_workflow(data_dir=None, subjects=None, name="fslwarp"):
"""Set up the anatomical normalzation workflow using FNIRT.
Your anatomical data must have been processed in Freesurfer.
Unlike most lyman workflows, the DataGrabber and DataSink
nodes are hardwired within the returned workflow, as this
tightly integrates with the Freesurfer subjects directory
structure.
Parameters
----------
data_dir : path
top level of data hierarchy/FS subjects directory
subjects : list of strings
list of subject IDs
name : alphanumeric string, optional
workflow name
"""
if data_dir is None:
data_dir = os.environ["SUBJECTS_DIR"]
if subjects is None:
subjects = []
# Get target images
target_brain = fsl.Info.standard_image("avg152T1_brain.nii.gz")
target_head = fsl.Info.standard_image("avg152T1.nii.gz")
hires_head = fsl.Info.standard_image("MNI152_T1_1mm.nii.gz")
target_mask = fsl.Info.standard_image(
"MNI152_T1_2mm_brain_mask_dil.nii.gz")
fnirt_cfg = os.path.join(os.environ["FSLDIR"],
"etc/flirtsch/T1_2_MNI152_2mm.cnf")
# Subject source node
subjectsource = Node(IdentityInterface(fields=["subject_id"]),
iterables=("subject_id", subjects),
name="subjectsource")
# Grab recon-all outputs
head_image = "T1"
templates = dict(aseg="{subject_id}/mri/aparc+aseg.mgz",
head="{subject_id}/mri/" + head_image + ".mgz")
datasource = Node(SelectFiles(templates, base_directory=data_dir),
"datasource")
# Convert images to nifti storage and float representation
cvtaseg = Node(fs.MRIConvert(out_type="niigz"), "convertaseg")
cvthead = Node(fs.MRIConvert(out_type="niigz", out_datatype="float"),
"converthead")
# Turn the aparc+aseg into a brainmask
makemask = Node(fs.Binarize(dilate=1, min=0.5), "makemask")
# Extract the brain from the orig.mgz using the mask
skullstrip = Node(fsl.ApplyMask(), "skullstrip")
# FLIRT brain to MNI152_brain
flirt = Node(fsl.FLIRT(reference=target_brain), "flirt")
sw = [-180, 180]
for dim in ["x", "y", "z"]:
setattr(flirt.inputs, "searchr_%s" % dim, sw)
# FNIRT head to MNI152
fnirt = Node(
fsl.FNIRT(ref_file=target_head,
refmask_file=target_mask,
config_file=fnirt_cfg,
fieldcoeff_file=True), "fnirt")
# Warp and rename the images
warpbrain = Node(
fsl.ApplyWarp(ref_file=target_head,
interp="spline",
out_file="brain_warp.nii.gz"), "warpbrain")
warpbrainhr = Node(
fsl.ApplyWarp(ref_file=hires_head,
interp="spline",
out_file="brain_warp_hires.nii.gz"), "warpbrainhr")
# Generate a png summarizing the registration
warpreport = Node(WarpReport(), "warpreport")
# Save relevant files to the data directory
fnirt_subs = [(head_image + "_out_masked_flirt.mat", "affine.mat"),
(head_image + "_out_fieldwarp", "warpfield"),
(head_image + "_out_masked", "brain"),
(head_image + "_out", "T1")]
datasink = Node(
DataSink(base_directory=data_dir,
parameterization=False,
substitutions=fnirt_subs), "datasink")
# Define and connect the workflow
# -------------------------------
normalize = Workflow(name=name)
normalize.connect([
(subjectsource, datasource, [("subject_id", "subject_id")]),
(datasource, cvtaseg, [("aseg", "in_file")]),
(datasource, cvthead, [("head", "in_file")]),
(cvtaseg, makemask, [("out_file", "in_file")]),
(cvthead, skullstrip, [("out_file", "in_file")]),
(makemask, skullstrip, [("binary_file", "mask_file")]),
(skullstrip, flirt, [("out_file", "in_file")]),
(flirt, fnirt, [("out_matrix_file", "affine_file")]),
(cvthead, fnirt, [("out_file", "in_file")]),
(skullstrip, warpbrain, [("out_file", "in_file")]),
(fnirt, warpbrain, [("fieldcoeff_file", "field_file")]),
(skullstrip, warpbrainhr, [("out_file", "in_file")]),
(fnirt, warpbrainhr, [("fieldcoeff_file", "field_file")]),
(warpbrain, warpreport, [("out_file", "in_file")]),
(subjectsource, datasink, [("subject_id", "container")]),
(skullstrip, datasink, [("out_file", "normalization.@brain")]),
(cvthead, datasink, [("out_file", "normalization.@t1")]),
(flirt, datasink, [("out_file", "normalization.@brain_flirted")]),
(flirt, datasink, [("out_matrix_file", "normalization.@affine")]),
(warpbrain, datasink, [("out_file", "normalization.@brain_warped")]),
(warpbrainhr, datasink, [("out_file", "normalization.@brain_hires")]),
(fnirt, datasink, [("fieldcoeff_file", "normalization.@warpfield")]),
(warpreport, datasink, [("out_file", "normalization.@report")]),
])
return normalize
def create_transform_pipeline(name='transfrom_timeseries'):
# set fsl output type
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# initiate workflow
transform_ts = Workflow(name='transform_timeseries')
# inputnode
inputnode=Node(util.IdentityInterface(fields=['orig_ts',
'anat_head',
'mat_moco',
'fullwarp',
'resolution',
'brain_mask'
]),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['trans_ts',
'trans_ts_mean',
'trans_ts_masked',
'resamp_brain',
'brain_mask_resamp',
'out_dvars'
]),
name='outputnode')
#resample anatomy
resample = Node(fsl.FLIRT(datatype='float',
out_file='T1_resampled.nii.gz'),
name = 'resample_anat')
transform_ts.connect([(inputnode, resample, [('anat_head', 'in_file'),
('anat_head', 'reference'),
('resolution', 'apply_isoxfm')
]),
(resample, outputnode, [('out_file', 'resamp_brain')])
])
# split timeseries in single volumes
split=Node(fsl.Split(dimension='t',
out_base_name='timeseries'),
name='split')
transform_ts.connect([(inputnode, split, [('orig_ts','in_file')])])
# applymoco premat and fullwarpfield
applywarp = MapNode(fsl.ApplyWarp(interp='spline',
relwarp=True,
out_file='rest2anat.nii.gz',
datatype='float'),
iterfield=['in_file', 'premat'],
name='applywarp')
transform_ts.connect([(split, applywarp, [('out_files', 'in_file')]),
(inputnode, applywarp,
[('mat_moco', 'premat'),
('fullwarp','field_file')]),
(resample, applywarp, [('out_file', 'ref_file')])
])
# re-concatenate volumes
merge=Node(fsl.Merge(dimension='t',
merged_file='rest2anat.nii.gz'),
name='merge')
transform_ts.connect([(applywarp,merge,[('out_file','in_files')]),
(merge, outputnode, [('merged_file', 'trans_ts')])])
# calculate new mean
tmean = Node(fsl.maths.MeanImage(dimension='T',
out_file='rest_mean2anat_lowres.nii.gz'),
name='tmean')
transform_ts.connect([(merge, tmean, [('merged_file', 'in_file')]),
(tmean, outputnode, [('out_file', 'trans_ts_mean')])
])
# resample brain mask
resample_brain = Node(afni.Resample(resample_mode='NN',
outputtype='NIFTI_GZ',
out_file='T1_brain_mask_lowres.nii.gz'),
name = 'resample_brain')
transform_ts.connect([(inputnode, resample_brain, [('brain_mask', 'in_file')]),
(tmean, resample_brain, [('out_file', 'master')]),
(resample_brain, outputnode, [('out_file', 'brain_mask_resamp')])
])
#mask the transformed file
mask = Node(fsl.ApplyMask(), name="mask")
transform_ts.connect([(resample_brain,mask, [('out_file', 'mask_file')]),
(merge, mask, [('merged_file', 'in_file')]),
(mask, outputnode, [('out_file', 'trans_ts_masked')])
])
#calculate DVARS
dvars = Node(confounds.ComputeDVARS(save_all=True, save_plot=True), name="dvars")
transform_ts.connect([(resample_brain, dvars, [('out_file', 'in_mask')]),
(merge, dvars, [('merged_file', 'in_file')]),
(dvars, outputnode, [('out_all', 'out_dvars')])
])
return transform_ts
def prep_for_fmriprep(bidsdir, rawdir, substr):
#make subject dir, anat and func
subid = substr.replace('-', '_').replace('_', '')
anatdir = bidsdir + '/sub-' + subid + '/anat/'
funcdir = bidsdir + '/sub-' + subid + '/func/'
os.makedirs(anatdir, exist_ok=True)
os.makedirs(funcdir, exist_ok=True)
# get t1brain and MNI template
t1brain = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/reg/highres.nii.gz' % substr
template = str(
get_template('MNI152NLin2009cAsym',
resolution=2,
desc='brain',
suffix='T1w',
extension=['.nii', '.nii.gz']))
## registered T1w to template for fmriprep standard
### this reg files may not be used
tranformfile = tempfile.mkdtemp()
reg = Registration()
reg.inputs.fixed_image = template
reg.inputs.moving_image = t1brain
reg.inputs.output_transform_prefix = tranformfile + '/t12mni_'
reg.inputs.transforms = ['Affine', 'SyN']
reg.inputs.transform_parameters = [(2.0, ), (0.25, 3.0, 0.0)]
reg.inputs.number_of_iterations = [[1500, 200], [100, 50, 30]]
reg.inputs.dimension = 3
reg.inputs.num_threads = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = False
reg.inputs.initialize_transforms_per_stage = True
reg.inputs.metric = ['Mattes'] * 2
reg.inputs.metric_weight = [
1
] * 2 # Default (value ignored currently by ANTs)
reg.inputs.radius_or_number_of_bins = [32] * 2
reg.inputs.sampling_strategy = ['Random', None]
reg.inputs.sampling_percentage = [0.05, None]
reg.inputs.convergence_threshold = [1.e-8, 1.e-9]
reg.inputs.convergence_window_size = [20] * 2
reg.inputs.smoothing_sigmas = [[1, 0], [2, 1, 0]]
reg.inputs.sigma_units = ['vox'] * 2
reg.inputs.shrink_factors = [[2, 1], [3, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True, True]
reg.inputs.use_histogram_matching = [True, True] # This is the default
#reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
reg.cmdline
reg.run()
## copy transform file to fmriprep directory
mni2twtransform = anatdir + '/sub-' + subid + '_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5'
t1w2mnitransform = anatdir + '/sub-' + subid + '_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5'
copyfile(tranformfile + '/t12mni_Composite.h5', t1w2mnitransform)
copyfile(tranformfile + '/t12mni_InverseComposite.h5', mni2twtransform)
### warp the non-processed/filtered/smooth bold to fmriprep
### now functional
boldmask = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/mask.nii.gz' % substr
boldref = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI_SBREF.nii.gz' % substr
boldprep = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.nii.gz' % substr
reffile = tempfile.mkdtemp() + '/reffile.nii.gz'
boldstd = reffile = tempfile.mkdtemp() + '/boldstd.nii.gz'
maskstd = reffile = tempfile.mkdtemp() + '/maskstd.nii.gz'
aw = fsl.ApplyWarp()
aw.inputs.in_file = boldref
aw.inputs.ref_file = template
aw.inputs.field_file = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/reg/example_func2standard_warp.nii.gz' % substr
aw.inputs.out_file = reffile
aw.inputs.output_type = 'NIFTI_GZ'
res = aw.run()
aw1 = fsl.ApplyWarp()
aw1.inputs.interp = 'spline'
aw1.inputs.ref_file = template
aw1.inputs.field_file = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/reg/example_func2standard_warp.nii.gz' % substr
aw1.inputs.in_file = boldprep
aw1.inputs.out_file = boldstd
aw1.inputs.output_type = 'NIFTI_GZ'
res1 = aw1.run()
aw2 = fsl.ApplyWarp()
aw2.inputs.in_file = boldmask
aw2.inputs.ref_file = template
aw2.inputs.field_file = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/reg/example_func2standard_warp.nii.gz' % substr
aw2.inputs.out_file = maskstd
aw2.inputs.output_type = 'NIFTI_GZ'
res2 = aw2.run()
tr = nb.load(boldprep).header.get_zooms()[-1]
jsontis = {
"RepetitionTime": np.float64(tr),
"TaskName": 'rest',
"SkullStripped": False,
}
jsmaks = {"mask": True}
#newname
preprocbold = funcdir + '/sub-' + subid + '_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'
preprocboldjson = funcdir + '/sub-' + subid + '_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json'
preprocboldref = funcdir + '/sub-' + subid + '_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz'
preprocmask = funcdir + '/sub-' + subid + '_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz'
preprocmaskjson = funcdir + '/sub-' + subid + '_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.json'
copyfile(maskstd, preprocmask)
copyfile(reffile, preprocboldref)
copyfile(boldstd, preprocbold)
writejson(jsontis, preprocboldjson)
writejson(jsmaks, preprocmaskjson)
# get wm and csf mask to extract mean signals for regressors
### first warp the anatomical to bold space
wmask = rawdir + '/UKB_Pipeline/%s/T1/T1_fast/T1_brain_pve_2.nii.gz' % substr
csfmask = rawdir + '/UKB_Pipeline/%s/T1/T1_fast/T1_brain_pve_0.nii.gz' % substr
t2funcwmask = tempfile.mkdtemp() + '/wmask.nii.gz'
t2funcwcsf = tempfile.mkdtemp() + '/csf.nii.gz'
aw = fsl.preprocess.ApplyXFM()
aw.inputs.in_file = wmask
aw.inputs.reference = boldref
aw.inputs.in_matrix_file = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/reg/highres2example_func.mat' % substr
aw.inputs.out_file = t2funcwmask
aw.inputs.apply_xfm = True
aw.inputs.interp = 'nearestneighbour'
aw.inputs.output_type = 'NIFTI_GZ'
res = aw.run()
aw2 = fsl.preprocess.ApplyXFM()
aw2.inputs.in_file = csfmask
aw2.inputs.reference = boldref
aw2.inputs.in_matrix_file = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/reg/highres2example_func.mat' % substr
aw2.inputs.out_file = t2funcwcsf
aw2.inputs.apply_xfm = True
aw2.inputs.interp = 'nearestneighbour'
aw2.inputs.output_type = 'NIFTI_GZ'
res2 = aw2.run()
# binarized and extract signals
wmbin = nb.load(t2funcwmask).get_fdata()
wmbin[wmbin < 0.99999] = 0
csfbin = nb.load(t2funcwcsf).get_fdata()
csfbin[csfbin < 0.99999] = 0
maskbin = nb.load(boldmask).get_fdata()
bolddata = nb.load(boldprep).get_fdata()
wm_mean = bolddata[wmbin > 0, :].mean(axis=0)
csf_mean = bolddata[csfbin > 0, :].mean(axis=0)
global_mean = bolddata[maskbin > 0, :].mean(axis=0)
#### combine all the regressors
mcfile = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/mc/prefiltered_func_data_mcf.par' % substr
rsmdfile = rawdir + '/UKB_Pipeline/%s/fMRI_nosmooth/rfMRI.ica/mc/prefiltered_func_data_mcf_abs.rms' % substr
motionfile = np.loadtxt(mcfile)
rsmd = np.loadtxt(rsmdfile)
motionparam = pd.DataFrame(
motionfile,
columns=['rot_x', 'rot_y', 'rot_z', 'trans_x', 'trans_y', 'trans_z'])
otherparam = pd.DataFrame({
'global_signal': global_mean,
'white_matter': wm_mean,
'csf': csf_mean,
'rmsd': rsmd
})
regressors = pd.concat([motionparam, otherparam], axis=1)
jsonreg = {'regressor': 'not'}
regcsv = funcdir + '/sub-' + subid + '_task-rest_desc-confounds_timeseries.tsv'
regjson = funcdir + '/sub-' + subid + '_task-rest_desc-confounds_timeseries.json'
regressors.to_csv(regcsv, index=None, sep='\t')
writejson(jsonreg, regjson)
def reg2std(name='standardization'):
"""
Linear and non-linear standardization for structural rat MRI images
Input: upscaled data
"""
reg = pe.Workflow(name=name)
"""
Set up a node to define all inputs required for the preprocessing workflow
"""
inputnode = pe.Node(interface=util.IdentityInterface(fields=['in_file_head', 'in_file_brain'], mandatory_inputs=True),
name='inputspec')
"""
Set up a node to define outputs for the preprocessing workflow
"""
outputnode = pe.Node(interface=util.IdentityInterface(fields=['out_nonlin_head', 'out_nonlin_brain', 'out_warpfield', 'out_lin_brain'], mandatory_inputs=True),
name='outputspec')
"""
Node for linear (12-param) reg
flirt -in $in -ref $std -dof 12 -omat $omat -bins 256 -cost $type -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
"""
flirt=pe.MapNode(interface=fsl.FLIRT(reference='/opt/shared/etc/std/new/standard-wistar_2mm_brain.nii.gz',
dof=12,
bins=256,
cost='corratio',
interp='trilinear'),
name='linear_standardization',
iterfield=['in_file']) #out_matrix_file?, searchr?
"""
Non-linear reg
fnirt --in=$in --ref=$std --aff=$init --iout=$out --miter=2,3 --infwhm=4,1 --reffwhm=2,0 --subsamp=8,1 --estint=1,1 --applyrefmask=1,1 --applyinmask=0,0 --lambda=200,500 --warpres=10,10,10 --intmod=global_non_linear --refmask=$refmask --fout=$warpingfield --interp=spline
"""
#TODO: parametrize standard template
fnirt=pe.MapNode(interface=fsl.FNIRT( \
ref_file='/opt/shared/etc/std/new/standard-wistar_2mm_brain.nii.gz', \
refmask_file='/opt/shared/etc/std/new/standard-wistar_2mm_brain_mask.nii.gz', \
max_nonlin_iter=[2,3], \
in_fwhm=[2,0], \
ref_fwhm=[2,0], \
subsampling_scheme=[8,1],\
apply_intensity_mapping=[1,1],\
apply_refmask=[1,1],\
apply_inmask=[0,0],\
regularization_lambda=[200,500],\
warp_resolution=(10,10,10),\
intensity_mapping_model='global_non_linear_with_bias',\
field_file=True),
name='nonlinear_standardization',
iterfield=['in_file', 'affine_file' ])
"""
Non-linear reg
fnirt --in=$in --ref=$std --aff=$init --iout=$out --miter=2,3 --infwhm=4,1 --reffwhm=2,0 --subsamp=8,1 --estint=1,1 --applyrefmask=1,1 --applyinmask=0,0 --lambda=200,500 --warpres=10,10,10 --intmod=global_non_linear --refmask=$refmask --fout=$warpingfield --interp=spline
"""
applyWarp=pe.MapNode(interface=fsl.ApplyWarp(), name="warp_brain",
iterfield=['in_file', 'ref_file', 'field_file'])
# TODO applywarp: brain
reg.connect(inputnode, "in_file_brain", flirt, "in_file")
reg.connect(flirt, "out_file", outputnode, "out_lin_brain")
reg.connect(inputnode, "in_file_head", fnirt, "in_file")
reg.connect(flirt, "out_matrix_file", fnirt, "affine_file")
reg.connect(inputnode, "in_file_brain", applyWarp, "in_file")
reg.connect(fnirt, "warped_file", applyWarp, "ref_file")
reg.connect(fnirt, "field_file", applyWarp, "field_file")
reg.connect(fnirt, "warped_file", outputnode, "out_nonlin_head")
reg.connect(applyWarp, "out_file", outputnode, "out_nonlin_brain")
reg.connect(fnirt, "field_file", outputnode, "out_warpfield")
return reg
def output_to_standard(workflow,
output_name,
strat,
num_strat,
pipeline_config_obj,
map_node=False,
input_image_type=0):
nodes = strat.get_nodes_names()
if 'apply_ants_warp_functional_to_standard' in nodes:
# ANTS WARP APPLICATION
# convert the func-to-anat linear warp from FSL FLIRT to
# ITK (ANTS) format
fsl_to_itk_convert = create_wf_c3d_fsl_to_itk(
input_image_type,
map_node,
name='{0}_fsl_to_itk_{1}'.format(output_name, num_strat))
# collect the list of warps into a single stack to feed into the
# ANTS warp apply tool
collect_transforms = create_wf_collect_transforms(
map_node,
name='{0}_collect_transforms_{1}'.format(output_name, num_strat))
# ANTS apply warp
apply_ants_warp = create_wf_apply_ants_warp(
map_node,
name='{0}_to_standard_{1}'.format(output_name, num_strat),
ants_threads=int(pipeline_config_obj.num_ants_threads))
apply_ants_warp.inputs.inputspec.dimension = 3
apply_ants_warp.inputs.inputspec.interpolation = 'Linear'
apply_ants_warp.inputs.inputspec.reference_image = \
pipeline_config_obj.template_brain_only_for_func
apply_ants_warp.inputs.inputspec.input_image_type = \
input_image_type
# affine from FLIRT func->anat linear registration
node, out_file = strat['functional_to_anat_linear_xfm']
workflow.connect(node, out_file, fsl_to_itk_convert,
'inputspec.affine_file')
# reference used in FLIRT func->anat linear registration
node, out_file = strat['anatomical_brain']
workflow.connect(node, out_file, fsl_to_itk_convert,
'inputspec.reference_file')
# output file to be converted
node, out_file = \
strat[output_name]
workflow.connect(node, out_file, fsl_to_itk_convert,
'inputspec.source_file')
# nonlinear warp from anatomical->template ANTS registration
node, out_file = strat['anatomical_to_mni_nonlinear_xfm']
workflow.connect(node, out_file, collect_transforms,
'inputspec.warp_file')
# linear initial from anatomical->template ANTS registration
node, out_file = strat['ants_initial_xfm']
workflow.connect(node, out_file, collect_transforms,
'inputspec.linear_initial')
# linear affine from anatomical->template ANTS registration
node, out_file = strat['ants_affine_xfm']
workflow.connect(node, out_file, collect_transforms,
'inputspec.linear_affine')
# rigid affine from anatomical->template ANTS registration
node, out_file = strat['ants_rigid_xfm']
workflow.connect(node, out_file, collect_transforms,
'inputspec.linear_rigid')
# converted FLIRT func->anat affine, now in ITK (ANTS) format
workflow.connect(fsl_to_itk_convert, 'outputspec.itk_transform',
collect_transforms, 'inputspec.fsl_to_itk_affine')
# output file to be converted
node, out_file = strat[output_name]
workflow.connect(node, out_file, apply_ants_warp,
'inputspec.input_image')
# collection of warps to be applied to the output file
workflow.connect(collect_transforms,
'outputspec.transformation_series', apply_ants_warp,
'inputspec.transforms')
strat.update_resource_pool({
'{0}_to_standard'.format(output_name):
(apply_ants_warp, 'outputspec.output_image')
})
strat.append_name(apply_ants_warp.name)
num_strat += 1
elif 'anat_mni_fnirt_register' in nodes:
# FSL WARP APPLICATION
if map_node:
apply_fsl_warp = pe.MapNode(interface=fsl.ApplyWarp(),
name='{0}_to_standard_{1}'.format(
output_name, num_strat),
iterfield=['in_file'])
else:
apply_fsl_warp = pe.Node(interface=fsl.ApplyWarp(),
name='{0}_to_standard_{1}'.format(
output_name, num_strat))
apply_fsl_warp.inputs.ref_file = \
pipeline_config_obj.template_skull_for_func
# output file to be warped
node, out_file = strat[output_name]
workflow.connect(node, out_file, apply_fsl_warp, 'in_file')
# linear affine from func->anat linear FLIRT registration
node, out_file = strat['functional_to_anat_linear_xfm']
workflow.connect(node, out_file, apply_fsl_warp, 'premat')
# nonlinear warp from anatomical->template FNIRT registration
node, out_file = strat['anatomical_to_mni_nonlinear_xfm']
workflow.connect(node, out_file, apply_fsl_warp, 'field_file')
strat.update_resource_pool({
'{0}_to_standard'.format(output_name): (apply_fsl_warp, 'out_file')
})
strat.append_name(apply_fsl_warp.name)
elif 'anat_mni_flirt_register' in nodes:
# FSL WARP APPLICATION
if map_node:
apply_anat_warp = pe.MapNode(interface=fsl.ApplyWarp(),
name='{0}_to_anat_{1}'.format(
output_name, num_strat),
iterfield=['in_file'])
apply_fsl_warp = pe.MapNode(interface=fsl.ApplyWarp(),
name='{0}_to_standard_{1}'.format(
output_name, num_strat),
iterfield=['in_file'])
else:
apply_anat_warp = pe.Node(interface=fsl.ApplyWarp(),
name='{0}_to_anat_{1}'.format(
output_name, num_strat))
apply_fsl_warp = pe.Node(interface=fsl.ApplyWarp(),
name='{0}_to_standard_{1}'.format(
output_name, num_strat))
node, out_file = strat['anatomical_brain']
workflow.connect(node, out_file, apply_anat_warp, 'ref_file')
apply_fsl_warp.inputs.ref_file = \
pipeline_config_obj.template_skull_for_func
# output file to be warped
node, out_file = strat[output_name]
workflow.connect(node, out_file, apply_anat_warp, 'in_file')
# linear affine from func->anat linear FLIRT registration
node, out_file = strat['functional_to_anat_linear_xfm']
workflow.connect(node, out_file, apply_anat_warp, 'premat')
# output file to be warped
workflow.connect(apply_anat_warp, 'out_file', apply_fsl_warp,
'in_file')
# nonlinear warp from anatomical->template FNIRT registration
node, out_file = strat['anatomical_to_mni_linear_xfm']
workflow.connect(node, out_file, apply_fsl_warp, 'premat')
strat.update_resource_pool({
'{0}_to_standard'.format(output_name): (apply_fsl_warp, 'out_file')
})
strat.append_name(apply_fsl_warp.name)
return strat