def dilF(input_file):
output_file = os.path.join(os.path.dirname(input_file), 'mask.nii.gz')
mydilf = fsl.DilateImage(in_file=input_file,
operation='max',
out_file=output_file)
print(mydilf.cmdline)
mydilf.run()
return output_file
def __init__(self, name, base_dir=None):
super(BrainExtractionWorkflow, self).__init__(name, base_dir)
# Segmentation
# ============
seg_node = npe.MapNode(name="Segmentation",
iterfield="data",
interface=spm.Segment())
seg_node.inputs.gm_output_type = [False, False, True]
seg_node.inputs.wm_output_type = [False, False, True]
seg_node.inputs.csf_output_type = [False, False, True]
add1_node = npe.MapNode(name="AddGMWM",
iterfield=["in_file", "operand_file"],
interface=fsl.BinaryMaths())
add1_node.inputs.operation = 'add'
add2_node = npe.MapNode(name="AddGMWMCSF",
iterfield=["in_file", "operand_file"],
interface=fsl.BinaryMaths())
add2_node.inputs.operation = 'add'
dil_node = npe.MapNode(name="Dilate",
iterfield="in_file",
interface=fsl.DilateImage())
dil_node.inputs.operation = 'mean'
ero_node = npe.MapNode(name="Erode",
iterfield="in_file",
interface=fsl.ErodeImage())
thre_node = npe.MapNode(name="Threshold",
iterfield="in_file",
interface=fsl.Threshold())
thre_node.inputs.thresh = 0.5
fill_node = npe.MapNode(name="Fill",
iterfield="in_file",
interface=fsl.UnaryMaths())
fill_node.inputs.operation = 'fillh'
mask_node = npe.MapNode(name="ApplyMask",
iterfield=["in_file", "mask_file"],
interface=fsl.ApplyMask())
mask_node.inputs.output_type = str("NIFTI")
self.connect([
(seg_node, add1_node, [('native_gm_image', 'in_file')]),
(seg_node, add1_node, [('native_wm_image', 'operand_file')]),
(seg_node, add2_node, [('native_csf_image', 'in_file')]),
(add1_node, add2_node, [('out_file', 'operand_file')]),
(add2_node, dil_node, [('out_file', 'in_file')]),
(dil_node, ero_node, [('out_file', 'in_file')]),
(ero_node, thre_node, [('out_file', 'in_file')]),
(thre_node, fill_node, [('out_file', 'in_file')]),
(fill_node, mask_node, [('out_file', 'mask_file')]),
])
def ants_getmask(name):
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
import nipype.interfaces.ants as ants
import nipype.interfaces.freesurfer as fs
wf = pe.Workflow(name=name)
inputspec = pe.Node(
niu.IdentityInterface(fields=['functional', 'structural']),
name='inputspec')
bet = pe.Node(fsl.BET(mask=True, remove_eyes=True), name='bet')
applymask = pe.Node(fs.ApplyMask(), name='applymask')
#flirt = pe.Node(fsl.FLIRT(),name='flirt')
#applyxfm_mask = pe.Node(fsl.ApplyXfm(interp='nearestneighbour',apply_xfm=True),name='applyxfm_mask')
#applyxfm_seg = pe.MapNode(fsl.ApplyXfm(interp='nearestneighbour',apply_xfm=True),name='applyxfm_seg',iterfield=['in_file'])
dilate = pe.Node(fsl.DilateImage(operation='mean'), name='dilate')
atropos = pe.Node(ants.Atropos(initialization='KMeans',
number_of_tissue_classes=3,
dimension=3),
name='atropos')
n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='n4corrections')
outputspec = pe.Node(niu.IdentityInterface(
fields=['mask', 'reg_file', 'segments', 'warped_struct']),
name='outputspec')
#create brain mask
wf.connect(inputspec, "structural", bet, "in_file")
#dilate bets mask a bit for atropos
wf.connect(bet, "mask_file", dilate, "in_file")
# apply dilated mask to img
wf.connect(dilate, 'out_file', applymask, 'mask_file')
wf.connect(inputspec, 'structural', applymask, 'in_file')
#N4 bias correction
wf.connect(applymask, "out_file", n4, 'input_image')
# atropos it
wf.connect(n4, "output_image", atropos, 'intensity_images')
wf.connect(dilate, 'out_file', atropos, 'mask_image')
return wf
def create_skullstrip_workflow(name="skullstrip"):
# Define the workflow inputs
inputnode = pe.Node(util.IdentityInterface(fields=["timeseries"]),
name="inputs")
# Mean the timeseries across the fourth dimension
meanfunc1 = pe.MapNode(fsl.MeanImage(),
iterfield=["in_file"],
name="meanfunc1")
# Skullstrip the mean functional image
stripmean = pe.MapNode(fsl.BET(mask=True, no_output=True, frac=0.3),
iterfield=["in_file"],
name="stripmean")
# Use the mask from skullstripping to strip each timeseries
maskfunc1 = pe.MapNode(fsl.ApplyMask(),
iterfield=["in_file", "mask_file"],
name="maskfunc1")
# Determine the 2nd and 98th percentile intensities of each run
getthresh = pe.MapNode(fsl.ImageStats(op_string="-p 2 -p 98"),
iterfield=["in_file"],
name="getthreshold")
# Threshold functional data at 10% of the 98th percentile
threshold = pe.MapNode(fsl.ImageMaths(out_data_type="char",
suffix="_thresh"),
iterfield=["in_file"],
name="threshold")
# Dilate the mask
dilatemask = pe.MapNode(fsl.DilateImage(operation="max"),
iterfield=["in_file"],
name="dilatemask")
# Mask the runs again with this new mask
maskfunc2 = pe.MapNode(fsl.ApplyMask(),
iterfield=["in_file", "mask_file"],
name="maskfunc2")
# Get a new mean image from each functional run
meanfunc2 = pe.MapNode(fsl.MeanImage(),
iterfield=["in_file"],
name="meanfunc2")
# Slice the mean func for reporting
meanslice = pe.MapNode(fsl.Slicer(image_width=800, label_slices=False),
iterfield=["in_file", "image_edges"],
name="meanslice")
meanslice.inputs.sample_axial = 2
# Rename the outputs
meanname = pe.MapNode(util.Rename(format_string="mean_func",
keep_ext=True),
iterfield=["in_file"],
name="meanname")
maskname = pe.MapNode(util.Rename(format_string="functional_mask",
keep_ext=True),
iterfield=["in_file"],
name="maskname")
pngname = pe.MapNode(util.Rename(format_string="mean_func.png"),
iterfield=["in_file"],
name="pngname")
# Define the workflow outputs
outputnode = pe.Node(util.IdentityInterface(
fields=["timeseries", "mean_func", "mask_file", "report_png"]),
name="outputs")
# Define and connect the workflow
skullstrip = pe.Workflow(name=name)
skullstrip.connect([
(inputnode, meanfunc1, [("timeseries", "in_file")]),
(meanfunc1, stripmean, [("out_file", "in_file")]),
(inputnode, maskfunc1, [("timeseries", "in_file")]),
(stripmean, maskfunc1, [("mask_file", "mask_file")]),
(maskfunc1, getthresh, [("out_file", "in_file")]),
(getthresh, threshold, [(("out_stat", get_thresh_op), "op_string")]),
(maskfunc1, threshold, [("out_file", "in_file")]),
(threshold, dilatemask, [("out_file", "in_file")]),
(inputnode, maskfunc2, [("timeseries", "in_file")]),
(dilatemask, maskfunc2, [("out_file", "mask_file")]),
(maskfunc2, meanfunc2, [("out_file", "in_file")]),
(meanfunc2, meanslice, [("out_file", "in_file")]),
(dilatemask, meanslice, [("out_file", "image_edges")]),
(meanslice, pngname, [("out_file", "in_file")]),
(meanfunc2, meanname, [("out_file", "in_file")]),
(dilatemask, maskname, [("out_file", "in_file")]),
(maskfunc2, outputnode, [("out_file", "timeseries")]),
(pngname, outputnode, [("out_file", "report_png")]),
(maskname, outputnode, [("out_file", "mask_file")]),
(meanname, outputnode, [("out_file", "mean_func")]),
])
return skullstrip
zeroing = pe.Node(interface=fsl.BinaryMaths(in_file=TemplateBrain,
operation='mul',
operand_value=0),
name='zeroing')
# Node for creating a point at the center of the ROI
addPoint = pe.Node(
interface=fsl.maths.MathsCommand( # Find a way to RegEx this
# args = '-add 1 -roi 45 1 74 1 51 1 0 1'
),
iterables=('args', ROIs),
name='addPoint')
# node for expanding the point
dilatePoint = pe.Node(interface=fsl.DilateImage(operation='mean',
kernel_shape='sphere',
kernel_size=5),
name='dilatePoint')
#DataSink --- stores important outputs
dataSink = pe.Node(
interface=nio.DataSink(
base_directory=ROIDir,
parameterization=
True # This line keeps the DataSink from adding an aditional level to the directory, I have no Idea why this works.
),
name="dataSink")
'''
###############
##Connections##
###############
def create_mask_from_seg_pipe(params={}, name="mask_from_seg_pipe"):
"""
Description: mask from segmentation tissues
#TODO To be added if required (was in old_segment before)
Function:
- Compute union of those 3 tissues;
- Apply morphological opening on the union mask
- Fill holes
Inputs:
mask_gm, mask_wm:
binary mask for grey matter and white matter
Outputs:
fill_holes.out_file:
filled mask after erode
fill_holes_dil.out_file
filled mask after dilate
"""
# creating pipeline
seg_pipe = pe.Workflow(name=name)
# Creating inputnode
inputnode = pe.Node(niu.IdentityInterface(
fields=['mask_gm', 'mask_wm', 'mask_csf', 'indiv_params']),
name='inputnode')
# bin_gm
bin_gm = pe.Node(interface=fsl.UnaryMaths(), name="bin_gm")
bin_gm.inputs.operation = "fillh"
seg_pipe.connect(inputnode, 'mask_gm', bin_gm, 'in_file')
# bin_csf
bin_csf = pe.Node(interface=fsl.UnaryMaths(), name="bin_csf")
bin_csf.inputs.operation = "fillh"
seg_pipe.connect(inputnode, 'mask_csf', bin_csf, 'in_file')
# bin_wm
bin_wm = pe.Node(interface=fsl.UnaryMaths(), name="bin_wm")
bin_wm.inputs.operation = "fillh"
seg_pipe.connect(inputnode, 'mask_wm', bin_wm, 'in_file')
# Compute union of the 3 tissues
# Done with 2 fslmaths as it seems to hard to do it
wmgm_union = pe.Node(fsl.BinaryMaths(), name="wmgm_union")
wmgm_union.inputs.operation = "add"
seg_pipe.connect(bin_gm, 'out_file', wmgm_union, 'in_file')
seg_pipe.connect(bin_wm, 'out_file', wmgm_union, 'operand_file')
tissues_union = pe.Node(fsl.BinaryMaths(), name="tissues_union")
tissues_union.inputs.operation = "add"
seg_pipe.connect(wmgm_union, 'out_file', tissues_union, 'in_file')
seg_pipe.connect(bin_csf, 'out_file', tissues_union, 'operand_file')
# Opening (dilating) mask
dilate_mask = NodeParams(fsl.DilateImage(),
params=parse_key(params, "dilate_mask"),
name="dilate_mask")
dilate_mask.inputs.operation = "mean" # Arbitrary operation
seg_pipe.connect(tissues_union, 'out_file', dilate_mask, 'in_file')
# fill holes of dilate_mask
fill_holes_dil = pe.Node(BinaryFillHoles(), name="fill_holes_dil")
seg_pipe.connect(dilate_mask, 'out_file', fill_holes_dil, 'in_file')
# Eroding mask
erode_mask = NodeParams(fsl.ErodeImage(),
params=parse_key(params, "erode_mask"),
name="erode_mask")
seg_pipe.connect(tissues_union, 'out_file', erode_mask, 'in_file')
# fill holes of erode_mask
fill_holes = pe.Node(BinaryFillHoles(), name="fill_holes")
seg_pipe.connect(erode_mask, 'out_file', fill_holes, 'in_file')
# merge to index
merge_indexed_mask = NodeParams(
interface=niu.Function(input_names=[
"mask_csf_file", "mask_wm_file", "mask_gm_file", "index_csf",
"index_gm", "index_wm"
],
output_names=['indexed_mask'],
function=merge_masks),
params=parse_key(params, "merge_indexed_mask"),
name="merge_indexed_mask")
seg_pipe.connect(bin_gm, 'out_file', merge_indexed_mask, "mask_gm_file")
seg_pipe.connect(bin_wm, 'out_file', merge_indexed_mask, "mask_wm_file")
seg_pipe.connect(bin_csf, 'out_file', merge_indexed_mask, "mask_csf_file")
return seg_pipe
NodeHash_20695ac0.inputs.percentage = 0.1 #Wraps command **fslmaths** NodeHash_10ff9c60 = pe.MapNode(interface = fsl.Threshold(), name = 'NodeName_10ff9c60', iterfield = ['in_file', 'thresh']) #Wraps command **fslmaths** NodeHash_843b4a0 = pe.MapNode(interface = fsl.MinImage(), name = 'NodeName_843b4a0', iterfield = ['in_file']) NodeHash_843b4a0.inputs.args = '-bin' NodeHash_843b4a0.inputs.dimension = 'T' #Wraps command **fslmaths** NodeHash_2b6977b0 = pe.MapNode(interface = fsl.ChangeDataType(), name = 'NodeName_2b6977b0', iterfield = ['in_file']) NodeHash_2b6977b0.inputs.output_datatype = 'char' #Wraps command **fslmaths** NodeHash_258767c0 = pe.MapNode(interface = fsl.DilateImage(), name = 'NodeName_258767c0', iterfield = ['in_file']) NodeHash_258767c0.inputs.operation = 'max' #Wraps command **fslstats** NodeHash_2fd0bda0 = pe.MapNode(interface = fsl.ImageStats(), name = 'NodeName_2fd0bda0', iterfield = ['in_file', 'mask_file']) NodeHash_2fd0bda0.inputs.op_string = '-p 50' #Wraps command **fslmaths** NodeHash_ffd7a90 = pe.MapNode(interface = fsl.ApplyMask(), name = 'NodeName_ffd7a90', iterfield = ['in_file', 'mask_file']) #Wraps command **fslmaths** NodeHash_255ee520 = pe.MapNode(interface = fsl.MeanImage(), name = 'NodeName_255ee520', iterfield = ['in_file']) #Custom interface wrapping function Getusan NodeHash_12d6d9d0 = pe.MapNode(interface = firstlevelhelpers.Getusan, name = 'NodeName_12d6d9d0', iterfield = ['brightness_thresh', 'in_file'])
def skullstrip_functional(skullstrip_tool='afni',
anatomical_mask_dilation=False,
wf_name='skullstrip_functional'):
skullstrip_tool = skullstrip_tool.lower()
if skullstrip_tool != 'afni' and skullstrip_tool != 'fsl' and skullstrip_tool != 'fsl_afni' and skullstrip_tool != 'anatomical_refined':
raise Exception(
"\n\n[!] Error: The 'tool' parameter of the "
"'skullstrip_functional' workflow must be either "
"'afni' or 'fsl' or 'fsl_afni' or 'anatomical_refined'.\n\nTool input: "
"{0}\n\n".format(skullstrip_tool))
wf = pe.Workflow(name=wf_name)
input_node = pe.Node(util.IdentityInterface(
fields=['func', 'anatomical_brain_mask', 'anat_skull']),
name='inputspec')
output_node = pe.Node(
util.IdentityInterface(fields=['func_brain', 'func_brain_mask']),
name='outputspec')
if skullstrip_tool == 'afni':
func_get_brain_mask = pe.Node(interface=preprocess.Automask(),
name='func_get_brain_mask_AFNI')
func_get_brain_mask.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'func', func_get_brain_mask, 'in_file')
wf.connect(func_get_brain_mask, 'out_file', output_node,
'func_brain_mask')
elif skullstrip_tool == 'fsl':
func_get_brain_mask = pe.Node(interface=fsl.BET(),
name='func_get_brain_mask_BET')
func_get_brain_mask.inputs.mask = True
func_get_brain_mask.inputs.functional = True
erode_one_voxel = pe.Node(interface=fsl.ErodeImage(),
name='erode_one_voxel')
erode_one_voxel.inputs.kernel_shape = 'box'
erode_one_voxel.inputs.kernel_size = 1.0
wf.connect(input_node, 'func', func_get_brain_mask, 'in_file')
wf.connect(func_get_brain_mask, 'mask_file', erode_one_voxel,
'in_file')
wf.connect(erode_one_voxel, 'out_file', output_node, 'func_brain_mask')
elif skullstrip_tool == 'fsl_afni':
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2,
mask=True,
functional=True),
name='skullstrip_first_pass')
bet_dilate = pe.Node(fsl.DilateImage(operation='max',
kernel_shape='sphere',
kernel_size=6.0,
internal_datatype='char'),
name='skullstrip_first_dilate')
bet_mask = pe.Node(fsl.ApplyMask(), name='skullstrip_first_mask')
unifize = pe.Node(afni_utils.Unifize(
t2=True,
outputtype='NIFTI_GZ',
args='-clfrac 0.2 -rbt 18.3 65.0 90.0',
out_file="uni.nii.gz"),
name='unifize')
skullstrip_second_pass = pe.Node(preprocess.Automask(
dilate=1, outputtype='NIFTI_GZ'),
name='skullstrip_second_pass')
combine_masks = pe.Node(fsl.BinaryMaths(operation='mul'),
name='combine_masks')
wf.connect([
(input_node, skullstrip_first_pass, [('func', 'in_file')]),
(skullstrip_first_pass, bet_dilate, [('mask_file', 'in_file')]),
(bet_dilate, bet_mask, [('out_file', 'mask_file')]),
(skullstrip_first_pass, bet_mask, [('out_file', 'in_file')]),
(bet_mask, unifize, [('out_file', 'in_file')]),
(unifize, skullstrip_second_pass, [('out_file', 'in_file')]),
(skullstrip_first_pass, combine_masks, [('mask_file', 'in_file')]),
(skullstrip_second_pass, combine_masks, [('out_file',
'operand_file')]),
(combine_masks, output_node, [('out_file', 'func_brain_mask')])
])
# Refine functional mask by registering anatomical mask to functional space
elif skullstrip_tool == 'anatomical_refined':
# Get functional mean to use later as reference, when transform anatomical mask to functional space
func_skull_mean = pe.Node(interface=afni_utils.TStat(),
name='func_skull_mean')
func_skull_mean.inputs.options = '-mean'
func_skull_mean.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'func', func_skull_mean, 'in_file')
# Register func to anat
linear_reg_func_to_anat = pe.Node(interface=fsl.FLIRT(),
name='linear_reg_func_to_anat')
linear_reg_func_to_anat.inputs.cost = 'mutualinfo'
linear_reg_func_to_anat.inputs.dof = 6
wf.connect(func_skull_mean, 'out_file', linear_reg_func_to_anat,
'in_file')
wf.connect(input_node, 'anat_skull', linear_reg_func_to_anat,
'reference')
# Inverse func to anat affine
inv_func_to_anat_affine = pe.Node(interface=fsl.ConvertXFM(),
name='inv_func_to_anat_affine')
inv_func_to_anat_affine.inputs.invert_xfm = True
wf.connect(linear_reg_func_to_anat, 'out_matrix_file',
inv_func_to_anat_affine, 'in_file')
# Transform anatomical mask to functional space
linear_trans_mask_anat_to_func = pe.Node(
interface=fsl.FLIRT(), name='linear_trans_mask_anat_to_func')
linear_trans_mask_anat_to_func.inputs.apply_xfm = True
linear_trans_mask_anat_to_func.inputs.cost = 'mutualinfo'
linear_trans_mask_anat_to_func.inputs.dof = 6
linear_trans_mask_anat_to_func.inputs.interp = 'nearestneighbour'
# Dialate anatomical mask, if 'anatomical_mask_dilation : True' in config file
if anatomical_mask_dilation:
anat_mask_dilate = pe.Node(interface=afni.MaskTool(),
name='anat_mask_dilate')
anat_mask_dilate.inputs.dilate_inputs = '1'
anat_mask_dilate.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'anatomical_brain_mask', anat_mask_dilate,
'in_file')
wf.connect(anat_mask_dilate, 'out_file',
linear_trans_mask_anat_to_func, 'in_file')
else:
wf.connect(input_node, 'anatomical_brain_mask',
linear_trans_mask_anat_to_func, 'in_file')
wf.connect(func_skull_mean, 'out_file', linear_trans_mask_anat_to_func,
'reference')
wf.connect(inv_func_to_anat_affine, 'out_file',
linear_trans_mask_anat_to_func, 'in_matrix_file')
wf.connect(linear_trans_mask_anat_to_func, 'out_file', output_node,
'func_brain_mask')
func_edge_detect = pe.Node(interface=afni_utils.Calc(),
name='func_extract_brain')
func_edge_detect.inputs.expr = 'a*b'
func_edge_detect.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'func', func_edge_detect, 'in_file_a')
if skullstrip_tool == 'afni':
wf.connect(func_get_brain_mask, 'out_file', func_edge_detect,
'in_file_b')
elif skullstrip_tool == 'fsl':
wf.connect(erode_one_voxel, 'out_file', func_edge_detect, 'in_file_b')
elif skullstrip_tool == 'fsl_afni':
wf.connect(combine_masks, 'out_file', func_edge_detect, 'in_file_b')
elif skullstrip_tool == 'anatomical_refined':
wf.connect(linear_trans_mask_anat_to_func, 'out_file',
func_edge_detect, 'in_file_b')
wf.connect(func_edge_detect, 'out_file', output_node, 'func_brain')
return wf
def create_workflow(self, flow, inputnode, outputnode):
# resampling diffusion image and setting output type to short
fs_mriconvert = pe.Node(interface=fs.MRIConvert(out_type='nii',out_file='diffusion_resampled.nii'),name="diffusion_resample")
fs_mriconvert.inputs.vox_size = self.config.resampling
fs_mriconvert.inputs.resample_type = self.config.interpolation
flow.connect([(inputnode,fs_mriconvert,[('diffusion','in_file')])])
fs_mriconvert_wm_mask = pe.Node(interface=fs.MRIConvert(out_type='nii',resample_type='nearest',out_file='wm_mask_resampled.nii'),name="mask_resample")
fs_mriconvert_wm_mask.inputs.vox_size = self.config.resampling
flow.connect([(inputnode,fs_mriconvert_wm_mask,[('wm_mask_registered','in_file')])])
if self.config.processing_tool != 'DTK':
fs_mriconvert_ROIs = pe.MapNode(interface=fs.MRIConvert(out_type='nii',resample_type='nearest'),name="ROIs_resample",iterfield=['in_file'])
fs_mriconvert_ROIs.inputs.vox_size = self.config.resampling
flow.connect([(inputnode,fs_mriconvert_ROIs,[('roi_volumes','in_file')])])
if self.config.dilate_rois:
dilate_rois = pe.MapNode(interface=fsl.DilateImage(),iterfield=['in_file'],name='dilate_rois')
dilate_rois.inputs.operation = 'modal'
flow.connect([
(fs_mriconvert_ROIs,dilate_rois,[("out_file","in_file")]),
(dilate_rois,outputnode,[("out_file","roi_volumes")])
])
else:
flow.connect([
(fs_mriconvert_ROIs,outputnode,[("out_file","roi_volumes")])
])
else:
flow.connect([
(inputnode,outputnode,[("roi_volumes","roi_volumes")])
])
# Reconstruction
if self.config.processing_tool == 'DTK':
recon_flow = create_dtk_recon_flow(self.config.dtk_recon_config)
flow.connect([
(inputnode,recon_flow,[('diffusion','inputnode.diffusion')]),
(fs_mriconvert,recon_flow,[('out_file','inputnode.diffusion_resampled')]),
])
elif self.config.processing_tool == 'MRtrix':
recon_flow = create_mrtrix_recon_flow(self.config.mrtrix_recon_config)
flow.connect([
(inputnode,recon_flow,[('diffusion','inputnode.diffusion')]),
(inputnode,recon_flow,[('grad','inputnode.grad')]),
(fs_mriconvert,recon_flow,[('out_file','inputnode.diffusion_resampled')]),
(fs_mriconvert_wm_mask, recon_flow,[('out_file','inputnode.wm_mask_resampled')]),
(recon_flow,outputnode,[("outputnode.FA","gFA")]),
])
elif self.config.processing_tool == 'Camino':
recon_flow = create_camino_recon_flow(self.config.camino_recon_config)
flow.connect([
(inputnode,recon_flow,[('diffusion','inputnode.diffusion')]),
(fs_mriconvert,recon_flow,[('out_file','inputnode.diffusion_resampled')]),
(fs_mriconvert_wm_mask, recon_flow,[('out_file','inputnode.wm_mask_resampled')]),
(recon_flow,outputnode,[("outputnode.FA","gFA")])
])
elif self.config.processing_tool == 'FSL':
recon_flow = create_fsl_recon_flow(self.config.fsl_recon_config)
flow.connect([
(fs_mriconvert,recon_flow,[('out_file','inputnode.diffusion_resampled')]),
(fs_mriconvert_wm_mask,recon_flow,[('out_file','inputnode.wm_mask_resampled')])
])
elif self.config.processing_tool == 'Gibbs':
recon_flow = create_gibbs_recon_flow(self.config.gibbs_recon_config)
flow.connect([
(fs_mriconvert,recon_flow,[("out_file","inputnode.diffusion_resampled")])
])
# Tracking
if self.config.processing_tool == 'DTK':
track_flow = create_dtb_tracking_flow(self.config.dtb_tracking_config)
flow.connect([
(inputnode, track_flow,[('wm_mask_registered','inputnode.wm_mask_registered')]),
(recon_flow, track_flow,[('outputnode.DWI','inputnode.DWI')])
])
elif self.config.processing_tool == 'MRtrix':
track_flow = create_mrtrix_tracking_flow(self.config.mrtrix_tracking_config)
flow.connect([
(fs_mriconvert_wm_mask, track_flow,[('out_file','inputnode.wm_mask_resampled')]),
(recon_flow, outputnode,[('outputnode.DWI','fod_file')]),
(recon_flow, track_flow,[('outputnode.DWI','inputnode.DWI'),('outputnode.grad','inputnode.grad')]),
(dilate_rois,track_flow,[('out_file','inputnode.gm_registered')])
#(recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
# if self.config.diffusion_model == 'Probabilistic':
# flow.connect([
# (dilate_rois,track_flow,[('out_file','inputnode.gm_registered')]),
# ])
flow.connect([
(track_flow,outputnode,[('outputnode.track_file','track_file')])
])
elif self.config.processing_tool == 'Camino':
track_flow = create_camino_tracking_flow(self.config.camino_tracking_config)
flow.connect([
(fs_mriconvert_wm_mask, track_flow,[('out_file','inputnode.wm_mask_resampled')]),
(recon_flow, track_flow,[('outputnode.DWI','inputnode.DWI'), ('outputnode.grad','inputnode.grad')])
])
if self.config.diffusion_model == 'Probabilistic':
flow.connect([
(dilate_rois,track_flow,[('out_file','inputnode.gm_registered')]),
])
flow.connect([
(track_flow,outputnode,[('outputnode.track_file','track_file')])
])
elif self.config.processing_tool == 'FSL':
track_flow = create_fsl_tracking_flow(self.config.fsl_tracking_config)
flow.connect([
(fs_mriconvert_wm_mask,track_flow,[('out_file','inputnode.wm_mask_resampled')]),
(dilate_rois,track_flow,[('out_file','inputnode.gm_registered')]),
(recon_flow,track_flow,[('outputnode.fsamples','inputnode.fsamples')]),
(recon_flow,track_flow,[('outputnode.phsamples','inputnode.phsamples')]),
(recon_flow,track_flow,[('outputnode.thsamples','inputnode.thsamples')]),
])
flow.connect([
(track_flow,outputnode,[("outputnode.targets","track_file")]),
])
elif self.config.processing_tool == 'Gibbs':
track_flow = create_gibbs_tracking_flow(self.config.gibbs_tracking_config)
flow.connect([
(fs_mriconvert_wm_mask, track_flow,[('out_file','inputnode.wm_mask_resampled')]),
(recon_flow,track_flow,[("outputnode.recon_file","inputnode.recon_file")]),
(track_flow,outputnode,[('outputnode.track_file','track_file')])
])
if self.config.processing_tool == 'DTK':
flow.connect([
(recon_flow,outputnode, [("outputnode.gFA","gFA"),("outputnode.skewness","skewness"),
("outputnode.kurtosis","kurtosis"),("outputnode.P0","P0")]),
(track_flow,outputnode, [('outputnode.track_file','track_file')])
])
temp_node = pe.Node(interface=util.IdentityInterface(fields=["diffusion_model"]),name="diffusion_model")
temp_node.inputs.diffusion_model = self.config.diffusion_model
flow.connect([
(temp_node,outputnode,[("diffusion_model","diffusion_model")])
])
def init_enhance_and_skullstrip_bold_wf(name='enhance_and_skullstrip_bold_wf',
omp_nthreads=1,
enhance_t2=False):
"""
This workflow takes in a :abbr:`BOLD (blood-oxygen level-dependant)`
:abbr:`fMRI (functional MRI)` average/summary (e.g. a reference image
averaging non-steady-state timepoints), and sharpens the histogram
with the application of the N4 algorithm for removing the
:abbr:`INU (intensity non-uniformity)` bias field and calculates a signal
mask.
Steps of this workflow are:
1. Calculate a conservative mask using Nilearn's ``create_epi_mask``.
2. Run ANTs' ``N4BiasFieldCorrection`` on the input
:abbr:`BOLD (blood-oxygen level-dependant)` average, using the
mask generated in 1) instead of the internal Otsu thresholding.
3. Calculate a loose mask using FSL's ``bet``, with one mathematical morphology
dilation of one iteration and a sphere of 6mm as structuring element.
4. Mask the :abbr:`INU (intensity non-uniformity)`-corrected image
with the latest mask calculated in 3), then use AFNI's ``3dUnifize``
to *standardize* the T2* contrast distribution.
5. Calculate a mask using AFNI's ``3dAutomask`` after the contrast
enhancement of 4).
6. Calculate a final mask as the intersection of 3) and 5).
7. Apply final mask on the enhanced reference.
.. workflow ::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.bold.util import init_enhance_and_skullstrip_bold_wf
wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=1)
**Parameters**
name : str
Name of workflow (default: ``enhance_and_skullstrip_bold_wf``)
omp_nthreads : int
number of threads available to parallel nodes
enhance_t2 : bool
perform logarithmic transform of input BOLD image to improve contrast
before calculating the preliminary mask
**Inputs**
in_file
BOLD image (single volume)
**Outputs**
bias_corrected_file
the ``in_file`` after `N4BiasFieldCorrection`_
skull_stripped_file
the ``bias_corrected_file`` after skull-stripping
mask_file
mask of the skull-stripped input file
out_report
reportlet for the skull-stripping
.. _N4BiasFieldCorrection: https://hdl.handle.net/10380/3053
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['mask_file', 'skull_stripped_file', 'bias_corrected_file']),
name='outputnode')
# Create a loose mask to avoid N4 internal's Otsu mask
n4_mask = pe.Node(MaskEPI(upper_cutoff=0.75,
enhance_t2=enhance_t2,
opening=1,
no_sanitize=True),
name='n4_mask')
# Run N4 normally, force num_threads=1 for stability (images are small, no need for >1)
n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3,
copy_header=True),
name='n4_correct',
n_procs=1)
# Create a generous BET mask out of the bias-corrected EPI
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2, mask=True),
name='skullstrip_first_pass')
bet_dilate = pe.Node(fsl.DilateImage(operation='max',
kernel_shape='sphere',
kernel_size=6.0,
internal_datatype='char'),
name='skullstrip_first_dilate')
bet_mask = pe.Node(fsl.ApplyMask(), name='skullstrip_first_mask')
# Use AFNI's unifize for T2 constrast & fix header
unifize = pe.Node(
afni.Unifize(
t2=True,
outputtype='NIFTI_GZ',
# Default -clfrac is 0.1, 0.4 was too conservative
# -rbt because I'm a Jedi AFNI Master (see 3dUnifize's documentation)
args='-clfrac 0.2 -rbt 18.3 65.0 90.0',
out_file="uni.nii.gz"),
name='unifize')
fixhdr_unifize = pe.Node(CopyXForm(), name='fixhdr_unifize', mem_gb=0.1)
# Run ANFI's 3dAutomask to extract a refined brain mask
skullstrip_second_pass = pe.Node(afni.Automask(dilate=1,
outputtype='NIFTI_GZ'),
name='skullstrip_second_pass')
fixhdr_skullstrip2 = pe.Node(CopyXForm(),
name='fixhdr_skullstrip2',
mem_gb=0.1)
# Take intersection of both masks
combine_masks = pe.Node(fsl.BinaryMaths(operation='mul'),
name='combine_masks')
# Compute masked brain
apply_mask = pe.Node(fsl.ApplyMask(), name='apply_mask')
workflow.connect([
(inputnode, n4_mask, [('in_file', 'in_files')]),
(inputnode, n4_correct, [('in_file', 'input_image')]),
(inputnode, fixhdr_unifize, [('in_file', 'hdr_file')]),
(inputnode, fixhdr_skullstrip2, [('in_file', 'hdr_file')]),
(n4_mask, n4_correct, [('out_mask', 'mask_image')]),
(n4_correct, skullstrip_first_pass, [('output_image', 'in_file')]),
(skullstrip_first_pass, bet_dilate, [('mask_file', 'in_file')]),
(bet_dilate, bet_mask, [('out_file', 'mask_file')]),
(skullstrip_first_pass, bet_mask, [('out_file', 'in_file')]),
(bet_mask, unifize, [('out_file', 'in_file')]),
(unifize, fixhdr_unifize, [('out_file', 'in_file')]),
(fixhdr_unifize, skullstrip_second_pass, [('out_file', 'in_file')]),
(skullstrip_first_pass, combine_masks, [('mask_file', 'in_file')]),
(skullstrip_second_pass, fixhdr_skullstrip2, [('out_file', 'in_file')
]),
(fixhdr_skullstrip2, combine_masks, [('out_file', 'operand_file')]),
(fixhdr_unifize, apply_mask, [('out_file', 'in_file')]),
(combine_masks, apply_mask, [('out_file', 'mask_file')]),
(combine_masks, outputnode, [('out_file', 'mask_file')]),
(apply_mask, outputnode, [('out_file', 'skull_stripped_file')]),
(n4_correct, outputnode, [('output_image', 'bias_corrected_file')]),
])
return workflow
#Wraps command **fslmaths**
NodeHash_179e1da0 = pe.MapNode(interface=fsl.MinImage(),
name='NodeName_179e1da0',
iterfield=['in_file'])
NodeHash_179e1da0.inputs.args = '-bin'
NodeHash_179e1da0.inputs.dimension = 'T'
#Wraps command **fslmaths**
NodeHash_1879dad0 = pe.MapNode(interface=fsl.ChangeDataType(),
name='NodeName_1879dad0',
iterfield=['in_file'])
NodeHash_1879dad0.inputs.output_datatype = 'char'
#Wraps command **fslmaths**
NodeHash_188ac400 = pe.MapNode(interface=fsl.DilateImage(),
name='NodeName_188ac400',
iterfield=['in_file'])
NodeHash_188ac400.inputs.operation = 'max'
#Wraps command **fslstats**
NodeHash_1a202720 = pe.MapNode(interface=fsl.ImageStats(),
name='NodeName_1a202720',
iterfield=['in_file', 'mask_file'])
NodeHash_1a202720.inputs.op_string = '-p 50'
#Wraps command **fslmaths**
NodeHash_19cad2d0 = pe.MapNode(interface=fsl.ApplyMask(),
name='NodeName_19cad2d0',
iterfield=['in_file', 'mask_file'])
NodeHash_14e3d7c0.inputs.percentage = 0.1 #Wraps command **fslmaths** NodeHash_157bd2b0 = pe.MapNode(interface = fsl.Threshold(), name = 'NodeName_157bd2b0', iterfield = ['in_file', 'thresh']) #Wraps command **fslmaths** NodeHash_15f74220 = pe.MapNode(interface = fsl.MinImage(), name = 'NodeName_15f74220', iterfield = ['in_file']) NodeHash_15f74220.inputs.args = '-bin' NodeHash_15f74220.inputs.dimension = 'T' #Wraps command **fslmaths** NodeHash_16d421a0 = pe.MapNode(interface = fsl.ChangeDataType(), name = 'NodeName_16d421a0', iterfield = ['in_file']) NodeHash_16d421a0.inputs.output_datatype = 'char' #Wraps command **fslmaths** NodeHash_1801caa0 = pe.MapNode(interface = fsl.DilateImage(), name = 'NodeName_1801caa0', iterfield = ['in_file']) NodeHash_1801caa0.inputs.operation = 'max' #Wraps command **fslstats** NodeHash_18508680 = pe.MapNode(interface = fsl.ImageStats(), name = 'NodeName_18508680', iterfield = ['in_file', 'mask_file']) NodeHash_18508680.inputs.op_string = '-p 50' #Wraps command **fslmaths** NodeHash_181e69e0 = pe.MapNode(interface = fsl.ApplyMask(), name = 'NodeName_181e69e0', iterfield = ['in_file', 'mask_file']) #Wraps command **fslmaths** NodeHash_182b4bf0 = pe.MapNode(interface = fsl.MeanImage(), name = 'NodeName_182b4bf0', iterfield = ['in_file']) #Custom interface wrapping function Getusan NodeHash_1a479090 = pe.MapNode(interface = firstlevelhelpers.Getusan, name = 'NodeName_1a479090', iterfield = ['brightness_thresh', 'in_file'])
def create_workflow(self, flow, inputnode, outputnode):
"""Create the stage worflow.
Parameters
----------
flow : nipype.pipeline.engine.Workflow
The nipype.pipeline.engine.Workflow instance of the Diffusion pipeline
inputnode : nipype.interfaces.utility.IdentityInterface
Identity interface describing the inputs of the stage
outputnode : nipype.interfaces.utility.IdentityInterface
Identity interface describing the outputs of the stage
See Also
--------
cmp.stages.diffusion.reconstruction.create_dipy_recon_flow
cmp.stages.diffusion.reconstruction.create_mrtrix_recon_flow
cmp.stages.diffusion.tracking.create_dipy_tracking_flow
cmp.stages.diffusion.tracking.create_mrtrix_tracking_flow
"""
if self.config.dilate_rois:
dilate_rois = pe.MapNode(interface=fsl.DilateImage(),
iterfield=["in_file"],
synchronize=True,
name="dilate_rois")
dilate_rois.inputs.operation = "modal"
if self.config.dilation_kernel == "Box":
kernel_size = 2 * self.config.dilation_radius + 1
dilate_rois.inputs.kernel_shape = "boxv"
dilate_rois.inputs.kernel_size = kernel_size
else:
extract_sizes = pe.Node(interface=ExtractImageVoxelSizes(),
name="extract_sizes")
flow.connect([(inputnode, extract_sizes, [("diffusion",
"in_file")])])
extract_sizes.run()
print("Voxel sizes : ", extract_sizes.outputs.voxel_sizes)
min_size = 100
for voxel_size in extract_sizes.outputs.voxel_sizes:
if voxel_size < min_size:
min_size = voxel_size
print("voxel size (min): %g" % min_size)
if self.config.dilation_kernel == "Gauss":
kernel_size = 2 * extract_sizes.outputs.voxel_sizes + 1
# FWHM criteria, i.e. sigma = FWHM / 2(sqrt(2ln(2)))
sigma = kernel_size / 2.355
dilate_rois.inputs.kernel_shape = "gauss"
dilate_rois.inputs.kernel_size = sigma
elif self.config.dilation_kernel == "Sphere":
radius = 0.5 * min_size + self.config.dilation_radius * min_size
dilate_rois.inputs.kernel_shape = "sphere"
dilate_rois.inputs.kernel_size = radius
# fmt: off
flow.connect([
(inputnode, dilate_rois, [("roi_volumes", "in_file")]),
(dilate_rois, outputnode, [("out_file", "roi_volumes")]),
])
# fmt: on
else:
# fmt: off
flow.connect([(inputnode, outputnode, [("roi_volumes",
"roi_volumes")])])
# fmt: on
if self.config.recon_processing_tool == "Dipy":
recon_flow = create_dipy_recon_flow(self.config.dipy_recon_config)
# fmt: off
flow.connect([
(inputnode, recon_flow, [("diffusion", "inputnode.diffusion")
]),
(inputnode, recon_flow, [("bvals", "inputnode.bvals")]),
(inputnode, recon_flow, [("bvecs", "inputnode.bvecs")]),
(
inputnode,
recon_flow,
[("diffusion", "inputnode.diffusion_resampled")],
),
(
inputnode,
recon_flow,
[("wm_mask_registered", "inputnode.wm_mask_resampled")],
),
(
inputnode,
recon_flow,
[("brain_mask_registered",
"inputnode.brain_mask_resampled")],
),
(recon_flow, outputnode, [("outputnode.FA", "FA")]),
(recon_flow, outputnode, [("outputnode.MD", "ADC")]),
(recon_flow, outputnode, [("outputnode.AD", "AD")]),
(recon_flow, outputnode, [("outputnode.RD", "RD")]),
(recon_flow, outputnode, [("outputnode.shore_maps",
"shore_maps")]),
(
recon_flow,
outputnode,
[("outputnode.mapmri_maps", "mapmri_maps")],
),
])
# fmt: on
elif self.config.recon_processing_tool == "MRtrix":
# TODO modify nipype tensormetric interface to get AD and RD maps
recon_flow = create_mrtrix_recon_flow(
self.config.mrtrix_recon_config)
# fmt: off
flow.connect([
(inputnode, recon_flow, [("diffusion", "inputnode.diffusion")
]),
(inputnode, recon_flow, [("grad", "inputnode.grad")]),
(
inputnode,
recon_flow,
[("diffusion", "inputnode.diffusion_resampled")],
),
(
inputnode,
recon_flow,
[("brain_mask_registered", "inputnode.wm_mask_resampled")],
),
(recon_flow, outputnode, [("outputnode.FA", "FA")]),
(recon_flow, outputnode, [("outputnode.ADC", "ADC")]),
(recon_flow, outputnode, [("outputnode.tensor", "tensor")]),
# (recon_flow,outputnode,[("outputnode.AD","AD")]),
# (recon_flow,outputnode,[("outputnode.RD","RD")]),
])
# fmt: on
if self.config.tracking_processing_tool == "Dipy":
track_flow = create_dipy_tracking_flow(
self.config.dipy_tracking_config)
if self.config.diffusion_imaging_model != "DSI":
# fmt: off
flow.connect([
(recon_flow, outputnode, [("outputnode.DWI", "fod_file")]),
(
recon_flow,
track_flow,
[("outputnode.model", "inputnode.model")],
),
(inputnode, track_flow, [("bvals", "inputnode.bvals")]),
(
recon_flow,
track_flow,
[("outputnode.bvecs", "inputnode.bvecs")],
),
# Diffusion resampled
(inputnode, track_flow, [("diffusion", "inputnode.DWI")]),
(
inputnode,
track_flow,
[("partial_volumes", "inputnode.partial_volumes")],
),
(
inputnode,
track_flow,
[("wm_mask_registered", "inputnode.wm_mask_resampled")
],
),
# (inputnode, track_flow,[('diffusion','inputnode.DWI')]),
(recon_flow, track_flow, [("outputnode.FA", "inputnode.FA")
]),
(
dilate_rois,
track_flow,
[("out_file", "inputnode.gm_registered")],
)
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
# fmt: on
else:
# fmt: off
flow.connect([
(recon_flow, outputnode, [("outputnode.fod", "fod_file")]),
(
recon_flow,
track_flow,
[("outputnode.fod", "inputnode.fod_file")],
),
(
recon_flow,
track_flow,
[("outputnode.model", "inputnode.model")],
),
(inputnode, track_flow, [("bvals", "inputnode.bvals")]),
(
recon_flow,
track_flow,
[("outputnode.bvecs", "inputnode.bvecs")],
),
# Diffusion resampled
(inputnode, track_flow, [("diffusion", "inputnode.DWI")]),
(
inputnode,
track_flow,
[("partial_volumes", "inputnode.partial_volumes")],
),
(
inputnode,
track_flow,
[("wm_mask_registered", "inputnode.wm_mask_resampled")
],
),
# (inputnode, track_flow,[('diffusion','inputnode.DWI')]),
(recon_flow, track_flow, [("outputnode.FA", "inputnode.FA")
]),
(
dilate_rois,
track_flow,
[("out_file", "inputnode.gm_registered")],
)
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
# fmt: on
if (self.config.dipy_tracking_config.use_act
and self.config.dipy_tracking_config.seed_from_gmwmi):
# fmt: off
flow.connect([
(
inputnode,
track_flow,
[("gmwmi_registered", "inputnode.gmwmi_file")],
),
])
# fmt: on
# fmt: off
flow.connect([(track_flow, outputnode, [("outputnode.track_file",
"track_file")])])
# fmt: on
elif (self.config.tracking_processing_tool == "MRtrix"
and self.config.recon_processing_tool == "MRtrix"):
track_flow = create_mrtrix_tracking_flow(
self.config.mrtrix_tracking_config)
# fmt: off
flow.connect([
(inputnode, track_flow, [("wm_mask_registered",
"inputnode.wm_mask_resampled")]),
(recon_flow, outputnode, [("outputnode.DWI", "fod_file")]),
(recon_flow, track_flow, [("outputnode.DWI", "inputnode.DWI"),
("outputnode.grad", "inputnode.grad")
]),
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
# fmt: on
if self.config.dilate_rois:
# fmt: off
flow.connect([(dilate_rois, track_flow,
[("out_file", "inputnode.gm_registered")])])
# fmt: on
else:
# fmt: off
flow.connect([(inputnode, track_flow,
[("roi_volumes", "inputnode.gm_registered")])])
# fmt: on
# fmt: off
flow.connect([
(
inputnode,
track_flow,
[("act_5tt_registered", "inputnode.act_5tt_registered")],
),
(
inputnode,
track_flow,
[("gmwmi_registered", "inputnode.gmwmi_registered")],
),
])
# fmt: on
# fmt: off
flow.connect([(track_flow, outputnode, [("outputnode.track_file",
"track_file")])])
# fmt: on
elif (self.config.tracking_processing_tool == "MRtrix"
and self.config.recon_processing_tool == "Dipy"):
track_flow = create_mrtrix_tracking_flow(
self.config.mrtrix_tracking_config)
if self.config.diffusion_imaging_model != "DSI":
# fmt: off
flow.connect([
(
inputnode,
track_flow,
[
("wm_mask_registered",
"inputnode.wm_mask_resampled"),
("grad", "inputnode.grad"),
],
),
(recon_flow, outputnode, [("outputnode.DWI", "fod_file")]),
(recon_flow, track_flow, [("outputnode.DWI",
"inputnode.DWI")]),
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
# fmt: on
else:
# fmt: off
flow.connect([
(
inputnode,
track_flow,
[
("wm_mask_registered",
"inputnode.wm_mask_resampled"),
("grad", "inputnode.grad"),
],
),
(recon_flow, outputnode, [("outputnode.fod", "fod_file")]),
(recon_flow, track_flow, [("outputnode.fod",
"inputnode.DWI")]),
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
# fmt: on
if self.config.dilate_rois:
# fmt: off
flow.connect([(
dilate_rois,
track_flow,
[("out_file", "inputnode.gm_registered")],
)])
# fmt: on
else:
# fmt: off
flow.connect([(
inputnode,
track_flow,
[("roi_volumes", "inputnode.gm_registered")],
)])
# fmt: on
# fmt: off
flow.connect([
(
inputnode,
track_flow,
[("act_5tt_registered", "inputnode.act_5tt_registered")],
),
(
inputnode,
track_flow,
[("gmwmi_registered", "inputnode.gmwmi_registered")],
),
])
# fmt: on
# fmt: off
flow.connect([(track_flow, outputnode, [("outputnode.track_file",
"track_file")])])
# fmt: on
temp_node = pe.Node(
interface=util.IdentityInterface(fields=["diffusion_model"]),
name="diffusion_model",
)
temp_node.inputs.diffusion_model = self.config.diffusion_model
# fmt: off
flow.connect([(temp_node, outputnode, [("diffusion_model",
"diffusion_model")])])
def create_workflow(self, flow, inputnode, outputnode):
"""Create the stage worflow.
Parameters
----------
flow : nipype.pipeline.engine.Workflow
The nipype.pipeline.engine.Workflow instance of the Diffusion pipeline
inputnode : nipype.interfaces.utility.IdentityInterface
Identity interface describing the inputs of the stage
outputnode : nipype.interfaces.utility.IdentityInterface
Identity interface describing the outputs of the stage
See Also
--------
cmp.stages.diffusion.reconstruction.create_dipy_recon_flow
cmp.stages.diffusion.reconstruction.create_mrtrix_recon_flow
cmp.stages.diffusion.tracking.create_dipy_tracking_flow
cmp.stages.diffusion.tracking.create_mrtrix_tracking_flow
"""
if self.config.dilate_rois:
dilate_rois = pe.MapNode(interface=fsl.DilateImage(), iterfield=[
'in_file'], name='dilate_rois')
dilate_rois.inputs.operation = 'modal'
if self.config.dilation_kernel == 'Box':
kernel_size = 2 * self.config.dilation_radius + 1
dilate_rois.inputs.kernel_shape = 'boxv'
dilate_rois.inputs.kernel_size = kernel_size
else:
extract_sizes = pe.Node(
interface=ExtractImageVoxelSizes(), name='extract_sizes')
flow.connect([
(inputnode, extract_sizes, [("diffusion", "in_file")])
])
extract_sizes.run()
print("Voxel sizes : ", extract_sizes.outputs.voxel_sizes)
min_size = 100
for voxel_size in extract_sizes.outputs.voxel_sizes:
if voxel_size < min_size:
min_size = voxel_size
print("voxel size (min): %g" % min_size)
if self.config.dilation_kernel == 'Gauss':
kernel_size = 2 * extract_sizes.outputs.voxel_sizes + 1
# FWHM criteria, i.e. sigma = FWHM / 2(sqrt(2ln(2)))
sigma = kernel_size / 2.355
dilate_rois.inputs.kernel_shape = 'gauss'
dilate_rois.inputs.kernel_size = sigma
elif self.config.dilation_kernel == 'Sphere':
radius = 0.5 * min_size + self.config.dilation_radius * min_size
dilate_rois.inputs.kernel_shape = 'sphere'
dilate_rois.inputs.kernel_size = radius
flow.connect([
(inputnode, dilate_rois, [("roi_volumes", "in_file")]),
(dilate_rois, outputnode, [("out_file", "roi_volumes")])
])
else:
flow.connect([
(inputnode, outputnode, [("roi_volumes", "roi_volumes")])
])
if self.config.recon_processing_tool == 'Dipy':
recon_flow = create_dipy_recon_flow(self.config.dipy_recon_config)
flow.connect([
(inputnode, recon_flow, [
('diffusion', 'inputnode.diffusion')]),
(inputnode, recon_flow, [('bvals', 'inputnode.bvals')]),
(inputnode, recon_flow, [('bvecs', 'inputnode.bvecs')]),
(inputnode, recon_flow, [
('diffusion', 'inputnode.diffusion_resampled')]),
(inputnode, recon_flow, [
('wm_mask_registered', 'inputnode.wm_mask_resampled')]),
(inputnode, recon_flow, [
('brain_mask_registered', 'inputnode.brain_mask_resampled')]),
(recon_flow, outputnode, [("outputnode.FA", "FA")]),
(recon_flow, outputnode, [("outputnode.MD", "ADC")]),
(recon_flow, outputnode, [("outputnode.AD", "AD")]),
(recon_flow, outputnode, [("outputnode.RD", "RD")]),
(recon_flow, outputnode, [
("outputnode.shore_maps", "shore_maps")]),
(recon_flow, outputnode, [
("outputnode.mapmri_maps", "mapmri_maps")]),
])
elif self.config.recon_processing_tool == 'MRtrix':
# TODO modify nipype tensormetric interface to get AD and RD maps
recon_flow = create_mrtrix_recon_flow(
self.config.mrtrix_recon_config)
flow.connect([
(inputnode, recon_flow, [
('diffusion', 'inputnode.diffusion')]),
(inputnode, recon_flow, [('grad', 'inputnode.grad')]),
(inputnode, recon_flow, [
('diffusion', 'inputnode.diffusion_resampled')]),
(inputnode, recon_flow, [
('brain_mask_registered', 'inputnode.wm_mask_resampled')]),
(recon_flow, outputnode, [("outputnode.FA", "FA")]),
(recon_flow, outputnode, [("outputnode.ADC", "ADC")]),
(recon_flow, outputnode, [("outputnode.tensor", "tensor")]),
# (recon_flow,outputnode,[("outputnode.AD","AD")]),
# (recon_flow,outputnode,[("outputnode.RD","RD")]),
])
if self.config.tracking_processing_tool == 'Dipy':
track_flow = create_dipy_tracking_flow(
self.config.dipy_tracking_config)
# print "Dipy tracking"
if self.config.diffusion_imaging_model != 'DSI':
flow.connect([
(recon_flow, outputnode, [('outputnode.DWI', 'fod_file')]),
(recon_flow, track_flow, [
('outputnode.model', 'inputnode.model')]),
(inputnode, track_flow, [('bvals', 'inputnode.bvals')]),
(recon_flow, track_flow, [
('outputnode.bvecs', 'inputnode.bvecs')]),
# Diffusion resampled
(inputnode, track_flow, [('diffusion', 'inputnode.DWI')]),
(inputnode, track_flow, [
('partial_volumes', 'inputnode.partial_volumes')]),
(inputnode, track_flow, [
('wm_mask_registered', 'inputnode.wm_mask_resampled')]),
# (inputnode, track_flow,[('diffusion','inputnode.DWI')]),
(recon_flow, track_flow, [
("outputnode.FA", "inputnode.FA")]),
(dilate_rois, track_flow, [
('out_file', 'inputnode.gm_registered')])
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
else:
flow.connect([
(recon_flow, outputnode, [('outputnode.fod', 'fod_file')]),
(recon_flow, track_flow, [
('outputnode.fod', 'inputnode.fod_file')]),
(recon_flow, track_flow, [
('outputnode.model', 'inputnode.model')]),
(inputnode, track_flow, [('bvals', 'inputnode.bvals')]),
(recon_flow, track_flow, [
('outputnode.bvecs', 'inputnode.bvecs')]),
# Diffusion resampled
(inputnode, track_flow, [('diffusion', 'inputnode.DWI')]),
(inputnode, track_flow, [
('partial_volumes', 'inputnode.partial_volumes')]),
(inputnode, track_flow, [
('wm_mask_registered', 'inputnode.wm_mask_resampled')]),
# (inputnode, track_flow,[('diffusion','inputnode.DWI')]),
(recon_flow, track_flow, [
("outputnode.FA", "inputnode.FA")]),
(dilate_rois, track_flow, [
('out_file', 'inputnode.gm_registered')])
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
if self.config.dipy_tracking_config.use_act and self.config.dipy_tracking_config.seed_from_gmwmi:
flow.connect([
(inputnode, track_flow, [
('gmwmi_registered', 'inputnode.gmwmi_file')]),
])
flow.connect([
(track_flow, outputnode, [
('outputnode.track_file', 'track_file')])
])
elif self.config.tracking_processing_tool == 'MRtrix' and self.config.recon_processing_tool == 'MRtrix':
track_flow = create_mrtrix_tracking_flow(
self.config.mrtrix_tracking_config)
flow.connect([
(inputnode, track_flow, [
('wm_mask_registered', 'inputnode.wm_mask_resampled')]),
(recon_flow, outputnode, [('outputnode.DWI', 'fod_file')]),
(recon_flow, track_flow, [
('outputnode.DWI', 'inputnode.DWI'), ('outputnode.grad', 'inputnode.grad')]),
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
if self.config.dilate_rois:
flow.connect([
(dilate_rois, track_flow, [
('out_file', 'inputnode.gm_registered')])
])
else:
flow.connect([
(inputnode, track_flow, [
('roi_volumes', 'inputnode.gm_registered')])
])
flow.connect([
(inputnode, track_flow, [
('act_5tt_registered', 'inputnode.act_5tt_registered')]),
(inputnode, track_flow, [
('gmwmi_registered', 'inputnode.gmwmi_registered')])
])
flow.connect([
(track_flow, outputnode, [
('outputnode.track_file', 'track_file')])
])
elif self.config.tracking_processing_tool == 'MRtrix' and self.config.recon_processing_tool == 'Dipy':
track_flow = create_mrtrix_tracking_flow(self.config.mrtrix_tracking_config)
if self.config.diffusion_imaging_model != 'DSI':
flow.connect([
(inputnode, track_flow, [('wm_mask_registered', 'inputnode.wm_mask_resampled'),
('grad', 'inputnode.grad')]),
(recon_flow, outputnode, [('outputnode.DWI', 'fod_file')]),
(recon_flow, track_flow, [
('outputnode.DWI', 'inputnode.DWI')]),
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
else:
flow.connect([
(inputnode, track_flow, [('wm_mask_registered', 'inputnode.wm_mask_resampled'),
('grad', 'inputnode.grad')]),
(recon_flow, outputnode, [('outputnode.fod', 'fod_file')]),
(recon_flow, track_flow, [
('outputnode.fod', 'inputnode.DWI')]),
# (recon_flow, track_flow,[('outputnode.SD','inputnode.SD')]),
])
if self.config.dilate_rois:
flow.connect([
(dilate_rois, track_flow, [
('out_file', 'inputnode.gm_registered')])
])
else:
flow.connect([
(inputnode, track_flow, [
('roi_volumes', 'inputnode.gm_registered')])
])
flow.connect([
(inputnode, track_flow, [
('act_5tt_registered', 'inputnode.act_5tt_registered')]),
(inputnode, track_flow, [
('gmwmi_registered', 'inputnode.gmwmi_registered')])
])
# if self.config.diffusion_model == 'Probabilistic':
# flow.connect([
# (dilate_rois,track_flow,[('out_file','inputnode.gm_registered')]),
# ])
flow.connect([
(track_flow, outputnode, [
('outputnode.track_file', 'track_file')])
])
temp_node = pe.Node(interface=util.IdentityInterface(
fields=["diffusion_model"]), name='diffusion_model')
temp_node.inputs.diffusion_model = self.config.diffusion_model
flow.connect([
(temp_node, outputnode, [("diffusion_model", "diffusion_model")])
])
def run_workflow():
# ------------------ Specify variables
ds_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
data_dir = ds_root
output_dir = 'skull-stripped-pre-mc'
working_dir = 'workingdirs/skull-strip-functionals'
subject_list = ['eddy']
session_list = ['20170511']
# ------------------ Input Files
infosource = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
]),
name="infosource")
infosource.iterables = [
('session_id', session_list),
('subject_id', subject_list),
]
# SelectFiles
templates = {
'masks':
'transformed-manual-func-mask/sub-{subject_id}/ses-{session_id}/func/'
# 'sub-{subject_id}_ses-{session_id}*run-01_bold_res-1x1x1'
'sub-{subject_id}_ses-{session_id}*_bold_res-1x1x1'
'_transformedmask.nii.gz',
'functionals':
# 'func_unwarp/sub-{subject_id}/ses-{session_id}/func/'
'resampled-isotropic-1mm/sub-{subject_id}/ses-{session_id}/func/'
# 'sub-{subject_id}_ses-{session_id}*run-01_bold_res-1x1x1_preproc'
'sub-{subject_id}_ses-{session_id}*_bold_res-1x1x1_preproc'
'.nii.gz',
}
inputfiles = Node(nio.SelectFiles(templates, base_directory=data_dir),
name="input_files")
# ------------------ Output Files
# Datasink
outputfiles = Node(nio.DataSink(base_directory=ds_root,
container=output_dir,
parameterization=True),
name="output_files")
# Use the following DataSink output substitutions
outputfiles.inputs.substitutions = [
('subject_id_', 'sub-'),
('session_id_', 'ses-'),
('/funcbrain/', '/'),
('_preproc_masked.nii.gz', '_brain.nii.gz'),
]
# Put result into a BIDS-like format
outputfiles.inputs.regexp_substitutions = [
(r'_ses-([a-zA-Z0-9]*)_sub-([a-zA-Z0-9]*)', r'sub-\2/ses-\1'),
(r'_funcbrain[0-9]*/', r'func/'),
]
# -------------------------------------------- Create Pipeline
workflow = Workflow(name='transform_manual_func_mask',
base_dir=os.path.join(ds_root, working_dir))
workflow.connect([(infosource, inputfiles, [
('subject_id', 'subject_id'),
('session_id', 'session_id'),
])])
dilmask = MapNode(fsl.DilateImage(
operation='mean',
kernel_shape=('boxv'),
kernel_size=7,
),
iterfield=['in_file'],
name='dilmask')
workflow.connect(inputfiles, 'masks', dilmask, 'in_file')
erode = MapNode(fsl.ErodeImage(
kernel_shape=('boxv'),
kernel_size=3,
),
iterfield=['in_file'],
name='erode')
workflow.connect(dilmask, 'out_file', erode, 'in_file')
funcbrain = MapNode(fsl.ApplyMask(),
iterfield=['in_file', 'mask_file'],
name='funcbrain')
workflow.connect(
erode,
'out_file',
funcbrain,
'mask_file',
)
workflow.connect(
inputfiles,
'functionals',
funcbrain,
'in_file',
)
workflow.connect(funcbrain, 'out_file', outputfiles, 'funcbrain')
workflow.stop_on_first_crash = True
workflow.keep_inputs = True
workflow.remove_unnecessary_outputs = False
workflow.write_graph()
workflow.run()
label_unmasked = Node(interface=IdentityInterface(fields=['label_unmasked']),
name="label_unmasked")
label_masked = Node(interface=IdentityInterface(fields=['label_masked']),
name="label_masked")
reference_region = Node(
interface=CombineROIs(ROI_groupings=list(reference_ROI_grouping.values())),
name="reference_region")
reference_region_inferior = Node(interface=fsl.ImageMaths(op_string=' -mul '),
name="reference_region_inferior")
brainmask = Node(interface=fsl.ImageMaths(op_string=' -bin',
suffix='_brainmask'),
name='brainmask')
dilate = Node(interface=fsl.DilateImage(operation='max',
kernel_shape='box',
kernel_size=3),
name='dilate')
difference = Node(interface=fsl.ImageMaths(op_string=' -sub ', suffix='_diff'),
name='difference')
difference_masked = Node(interface=fsl.ImageMaths(op_string=' -mul ',
suffix='_mul'),
name='difference_masked')
add = Node(interface=fsl.ImageMaths(op_string=' -add ', suffix='_add'),
name='add')
multiply = Node(interface=fsl.ImageMaths(op_string=' -mul ', suffix='_mul'),
name='multiply')
pvc_labels = Node(
interface=CombineROIs(ROI_groupings=list(pvc_ROI_groupings.values())),
name="pvc_labels")
def main(data_dict, config_dict):
print()
# ~~~~~~ SET UP GLOBAL VARIABLES ~~~~~~
data_folder = data_dict['data folder']
data_list = data_dict['data list']
if len(data_list) != 0:
parent_logger.info('MOSAICS main analysis beginning, please wait.')
# # save directory
save_dir_parent = str(data_dict['save_dir'])
# dilate variable
dilate = int(config_dict['dilate'])
# smooth variable
smooth = int(config_dict['smooth'])
# MEP threshold
MEP_thresh = int(config_dict['MEP_threshold'])
# Grid spacing
grid_spacing = int(data_dict['grid spacing'])
file_atlas = str(config_dict['atlas'])
# Initialize a list before our for loop so we can create a dataframe to
# output for our results spreadsheet!
results_column_names = [
'Subject File Name', 'Muscle', 'Hotspot X', 'Hotspot Y',
'Hotspot Z', 'Max MEP', 'COM X', 'COM Y', 'COM Z',
'Map area (mm^2)', 'Map volume (mm^2 * mV)', 'SD Hotspot X',
'SD Hotspot Y', 'SD Hotspot Z', 'SD COM X', 'SD COM Y', 'SD COM Z',
'Coordinates Used', 'Dilation (mm)', 'Smoothing kernel (mm)',
'MEP threshold (%)'
]
results_metrics_list = list()
for subject in data_list:
# ~~~~~~SET UP SUBJECT-SPECIFIC VARIABLES~~~~~~
# data_list constructed, and these variables determined, by mos_find_datasets.py
# tag = subj name, stim_name = name of stimulation data (everything before .xls(x) extension),
# structural = nii*, stim_data = xls*
tag = subject[0]
file_t1 = os.path.join(data_folder, subject[1])
file_nibs_map = os.path.join(data_folder, subject[2])
#save directory, including sub-directory for each subject
save_dir = str(data_dict['save_dir'] + '/' + tag)
# # Create output directory
os.makedirs(save_dir, exist_ok=True)
# ~~~~~~THINGS TO DO ONCE PER SUBJECT~~~~~~
parent_logger.info('')
parent_logger.info('processing ' + tag + ', stim data: ' +
file_nibs_map)
# ~~~~~~LOAD DATA~~~~~~
# Read in a 1mm isotropic T1-weighted MRI .nii
data_T1 = nib.load(file_t1)
# ~~~~~~STRIP T1 image~~~~~~
# reminder, brainmask check = 0 if user does not provide their own brainmask and
# MOSAICS is to devise its own (we use default BET settings)
if data_dict['brainmask check'].get() == 0:
# if and elif check if brainmask exists in data folder and save dir (in that order)
# if it doesn't exist, run BET skullstripping
if os.path.isfile(
os.path.join(data_folder,
tag + data_dict['brainmask suffix'])):
ps_brainmask = os.path.abspath(
os.path.join(data_folder,
tag + data_dict['brainmask suffix']))
elif os.path.isfile(
os.path.join(save_dir,
tag + data_dict['brainmask suffix'])):
ps_brainmask = os.path.abspath(
os.path.join(save_dir,
tag + data_dict['brainmask suffix']))
else:
parent_logger.info('performing BET skull stripping')
ps_brainmask = mos_skullstrip.main(tag, file_t1,
data_folder, save_dir)
elif data_dict['brainmask check'].get() == 1:
# if and elif check if brainmask exists in data folder and save dir (in that order)
# if it doesn't exist, run BET skullstripping
if os.path.isfile(
os.path.join(data_folder,
tag + data_dict['brainmask suffix'])):
ps_brainmask = os.path.abspath(
os.path.join(data_folder,
tag + data_dict['brainmask suffix']))
elif os.path.isfile(
os.path.join(save_dir,
tag + data_dict['brainmask suffix'])):
ps_brainmask = os.path.abspath(
os.path.join(save_dir,
tag + data_dict['brainmask suffix']))
else:
parent_logger.warning(
'supplied brainmask not found, creating our own.')
parent_logger.info('performing BET skull stripping')
ps_brainmask = mos_skullstrip.main(tag, file_t1,
data_folder, save_dir)
##### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##### ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##### ~~~~~~~~~~~~~~~~~~~ Muscle loop starts below here
stim_dict = mos_load_data_multi_muscle.main(file_nibs_map)
locs_dict = stim_dict['locs']
muscles_dict = stim_dict[
'muscles'] # muscles_dict[0] = MEP data, [1] = responsive yes or no
for muscle in muscles_dict:
parent_logger.info('processing ' + muscle + ' data')
# establish save file names PER MUSCLE
file_grid = os.path.join(save_dir,
tag + '_' + muscle + '_grid.nii.gz')
file_samples = os.path.join(
save_dir, tag + '_' + muscle + '_samples.nii.gz')
file_responses = os.path.join(
save_dir, tag + '_' + muscle + '_responses.nii.gz')
# Noscale (below) is the initial heatmap, gets warped to standard space used
file_heatmap_ps_initial = os.path.join(
save_dir, tag + '_' + muscle + '_heatmap_initial.nii')
# Nomask includes weighted MEP values for heatmap, and is masked by fsl.ApplyMask() on line ~237
file_heatmap_ps_weighted = os.path.join(
save_dir, tag + '_' + muscle + '_heatmap_weighted.nii')
# Below variable is used on line 236
file_heatmap_ps_final = os.path.join(
save_dir, tag + '_' + muscle + '_heatmap.nii.gz')
file_heatmap_sd = os.path.join(
save_dir, tag + '_' + muscle + '_warped_heatmap.nii.gz')
# ~~~~~~SET UP STIM DATA ARRAYS~~~~~~
# Create an array of zeroes equal to size of T1 image, to initialize our output images
# What are these maps (below)?
# - map_responses = MEP amplitude overlayed in an array the same size as the T1 image, dilated across 5 voxels
# (so 5mm isotropic) in the script
# - map_samples = the same as responses, but no dilation, so 1mm isotropic?
# - map_grid = 'binary' mask, 0 or 99, which points had a stim? Originally
# also points orthogonally adjacent to each stim point are 1 instead of 99.
# the dict, map_outputs, contains the matrix arrays for each image
#map_outputs = initialize_stim_arrays(data_T1, data_nibs_map, MEP_thresh)
map_outputs = initialize_stim_arrays(data_T1, locs_dict,
muscles_dict, muscle,
MEP_thresh)
map_grid = map_outputs['grid']
map_samples = map_outputs['samples']
map_responses = map_outputs['responses']
# ~~~~~~SAVE RESPONSE MAP SO WE CAN DILATE~~~~~~
# save_map(file_responses, map_responses, data_T1)
save_map(file_samples, map_samples, data_T1)
"""
--- DEV NOTE ---
Need to ensure that borders between MEPs are maintained, no values are overwritten if dilation is too large
- if user inputs resolution in configure GUI, we can check if dilation is too large for the voxel size?
"""
# ~~~~~~RESLICE STRUCTURAL AND STIM IMAGES~~~~~~
# nibabel.processing.conform(data_T1) produces a 1mm isotropic, 256x256x256 image
# above also reorients the image to RAS which is something I guess.
# - Not implemented yet. Helen has notes in Slack I have not read yet.
# ~~~~~~DILATE STIMULATION DATA (MAP_RESPONSES)~~~~~~
parent_logger.info('dilating stimulation coordinates by ' +
str(config_dict['dilate']) + ' voxels')
if not os.path.isfile(file_responses):
map_responses_dilate = fsl.DilateImage()
map_responses_dilate.inputs.in_file = file_samples
map_responses_dilate.inputs.operation = 'max'
map_responses_dilate.inputs.kernel_shape = 'sphere'
map_responses_dilate.inputs.kernel_size = dilate
map_responses_dilate.inputs.out_file = file_responses
map_responses_temp = map_responses_dilate.run()
else:
parent_logger.info(
'dilation already done, skipping this step')
# Re-load the responses map, to receive the dilated version of the map
map_responses = nib.load(file_responses).get_fdata()
# ~~~~~~FLIP MAPS ANTERIOR/POSTERIOR IF BRAINSIGHT COORDINATES USED~~~~~~
# Rotate matrices in the y dimension (AP) to convert from RPS (Brainsight) to RAS (Nifti)
# RPS = +x is right, +y is posterior, +z is superior
# RAS = +x is right, +y is anterior, +z is superior
if data_dict['stim_coords'].get() == "Brainsight":
parent_logger.info(
'flipping coordinates of stimulations along anterior-posterior axis'
)
map_responses = np.flip(map_responses, 1)
map_samples = np.flip(map_samples, 1)
map_grid = np.flip(map_grid, 1)
# ~~~~~~PRODUCE HEATMAP~~~~~~
# Smooth the hotspot map using a 3D Gaussian
# Interestingly, FWHM = 2.355 * s.d. for Gaussian distribution, so divide smooth by 2.355 to get s.d.
parent_logger.info('producing heatmap of responsive sites')
stdev_gaussian = smooth / 2.355
map_heatmap_ps_initial = ndi.gaussian_filter(map_responses,
stdev_gaussian,
0,
mode='reflect')
# ~~~~~~WEIGHT MEPs~~~~~~
parent_logger.info('normalizing response map (by hotspot MEP)')
MEP_ps_max, map_responses_weighted, map_heatmap_ps_weighted =\
normalize_ps_heatmap(map_heatmap_ps_initial, map_samples, map_responses)
# ~~~~~~SAVE PATIENT SPACE FILES~~~~~~
# Stimulations: MEP amplitudes within a matrix sized to match structural image.
# Stimulations from experiment have been uniformaly dilated by the 'dilate' integer.
# Heatmap: Stimulations map with a gaussian filter applied to smooth the data
parent_logger.info(
'saving stimulation sites (grid), responsive sites (responses), and heatmap (heatmap)'
)
save_map(file_grid, map_grid, data_T1)
save_map(file_responses, map_responses_weighted, data_T1)
save_map(file_heatmap_ps_initial, map_heatmap_ps_initial,
data_T1)
save_map(file_heatmap_ps_weighted, map_heatmap_ps_weighted,
data_T1)
# remove samples map as we don't actually want the users to see it, only useful for development
if os.path.exists(file_samples):
os.remove(file_samples)
# ~~~~~~MASK HEATMAP MAPS IN PATIENT SPACE~~~~~~
# Heatmap: apply brain mask to limit smoothing into skull / scalp
# native space mask application
parent_logger.info(
'applying brainmask to patient-space heatmap')
mask_heatmap(file_heatmap_ps_weighted, ps_brainmask,
file_heatmap_ps_final)
# ~~~~~~CALCULATE METRICS (patient space)~~~~~~
# load back in masked heatmap to calculate metrics
map_heatmap_masked = nib.load(
file_heatmap_ps_final).get_fdata()
# HOTSPOT:
# raw MEP from the stim data, and smoothed (post-Gaussian filter), needed to normalize patient heatmap
results_ps_hotspot = np.unravel_index(
np.argmax(map_heatmap_masked), map_heatmap_masked.shape)
# CENTER OF MASS:
# convenient method from scipy / ndimage (imported as ndi)
results_ps_center_mass = ndi.measurements.center_of_mass(
map_heatmap_masked)
# MAP AREA:
#number of spots where a responsive MEP was observed
nonzero_responses = np.count_nonzero(map_samples)
ps_map_area = nonzero_responses * (grid_spacing**2)
# MAP VOLUME:
ps_map_volume = 0
# for all non-zero values (non-zero MEPs) in our array of mapped regions
for i in map_samples[np.nonzero(map_samples)]:
ps_map_volume = ps_map_volume + (i * (grid_spacing**2))
# ~~~~~~REPEAT RELEVANT STEPS IF DATA NORMALIZED~~~~~~
# Note this has to come after saving the initial files, as warps are applied to the heatmap
if config_dict['normalize'].get() == 1:
parent_logger.info(
'normalizing heatmap to standard space (SD)')
# -- register and establish name of the warped map, for functions below
parent_logger.info('atlas chosen: ' + file_atlas)
mos_warp_to_mni.main(tag, muscle, data_folder, save_dir,
file_t1, file_heatmap_ps_weighted,
file_atlas)
# -- standard space mask application to heatmap
parent_logger.info(
'applying brainmask to standard-space heatmap')
mask_heatmap(file_heatmap_sd,
str(config_dict['atlas mask']),
file_heatmap_sd)
# -- load in normalized heatmap to calculate some metrics
data_heatmap_warped = nib.load(file_heatmap_sd)
map_heatmap_warped = data_heatmap_warped.get_fdata()
# -- calculate standard space (sd) hotspot
results_sd_hotspot = np.unravel_index(
np.argmax(map_heatmap_warped),
map_heatmap_warped.shape)
MEP_sd_smoothed = map_heatmap_warped[results_sd_hotspot]
# -- calculate standard space center of gravity
results_sd_center_mass = ndi.measurements.center_of_mass(
map_heatmap_warped)
# Replace tuple with
## Probably don't need this unrounded tuple bit, no changes made
# rounded_sd_center_mass = (results_sd_center_mass[0],
# results_sd_center_mass[1],
# results_sd_center_mass[2])
# results_sd_center_mass = (round(results_sd_center_mass[0]),
# round(results_sd_center_mass[1]),
# round(results_sd_center_mass[2]))
# -- Convert standard space hotspot / COM from voxel coordinates to SD anatomical coords (mm)
atlas_affine = nib.load(file_atlas)
atlas_affine = atlas_affine.affine
## Hotspot
results_sd_hotspot = apply_affine(atlas_affine,
results_sd_hotspot)
## COM
results_sd_center_mass = apply_affine(
atlas_affine, results_sd_center_mass)
rounded_sd_center_mass = list()
rounded_sd_center_mass.append(
round(results_sd_center_mass[0], 2))
rounded_sd_center_mass.append(
round(results_sd_center_mass[1], 2))
rounded_sd_center_mass.append(
round(results_sd_center_mass[2], 2))
# normalize MEPs / intensity values for standard space heatmap
map_heatmap_sd_normal = (map_heatmap_warped /
MEP_sd_smoothed) * 100
# Overwrite previously warped, masked heatmap with a new, weighted MEP version
# parent_logger.info('weighting MEPs of standard-space heatmap')
file_heatmap_sd_normal = os.path.join(
save_dir, tag + '_warped_heatmap.nii.gz')
nii_heatmap_sd_normal = nib.Nifti1Image(
map_heatmap_sd_normal, data_heatmap_warped.affine)
nib.save(nii_heatmap_sd_normal, file_heatmap_sd_normal)
# standard space values are added to dict below, on line 292
else:
# put n/a values in correct dict locations
results_sd_hotspot = ('-', '-', '-')
results_sd_center_mass = ('-', '-', '-')
rounded_sd_center_mass = ('-', '-', '-')
# ~~~~~~OUTPUT SUBJECT METRICS TO RESULTS SPREADSHEET~~~~~~
# Make a list of this subject's values, then append it to the overall results list
# Variable order set on line 69 above (results_column_names):
# Participant, Image File, Stim file, MEP threshold, Hotspot X, Y, Z, Hotspot MEP, COG X, Y, Z,
# Standard hotspot X, Y, Z, Standard COG X, Y, Z
measures_list = [
tag, muscle, results_ps_hotspot[0], results_ps_hotspot[1],
results_ps_hotspot[2], MEP_ps_max,
round(results_ps_center_mass[0], 2),
round(results_ps_center_mass[1], 2),
round(results_ps_center_mass[2], 2), ps_map_area,
ps_map_volume, results_sd_hotspot[0],
results_sd_hotspot[1], results_sd_hotspot[2],
rounded_sd_center_mass[0], rounded_sd_center_mass[1],
rounded_sd_center_mass[2], data_dict['stim_coords'].get(),
str(dilate),
str(smooth),
str(MEP_thresh)
]
results_metrics_list.append(measures_list)
#clean up files, put into a separate function, see if that helps track everything
file_cleanup(file_heatmap_ps_initial, file_heatmap_ps_weighted,
save_dir, tag)
parent_logger.info('analysis completed for ' + tag + ' ' +
muscle)
print()
# ~~~~~~print values to spreadsheet after the loop has completed~~~~~~
metrics_dataframe = pd.DataFrame(results_metrics_list,
columns=results_column_names)
measures_file = os.path.join(save_dir_parent, 'mapping_results.xlsx')
metrics_dataframe.to_excel(measures_file)
parent_logger.info('MOSAICS main analysis completed successfully!')
else:
parent_logger.error(
'No subjects found for processing, MOSAICS processing not run')
def fsl_getmask(name):
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
wf = pe.Workflow(name=name)
inputspec = pe.Node(
niu.IdentityInterface(fields=['functional', 'structural']),
name='inputspec')
bet = pe.Node(fsl.BET(mask=True, remove_eyes=True), name='bet')
flirt = pe.Node(fsl.FLIRT(dof=6), name='flirt')
flirt_inv = flirt.clone('func2struct')
applyxfm_mask = pe.Node(fsl.ApplyXfm(interp='nearestneighbour',
apply_xfm=True),
name='applyxfm_mask')
applyxfm_seg = pe.MapNode(fsl.ApplyXfm(interp='nearestneighbour',
apply_xfm=True),
name='applyxfm_seg',
iterfield=['in_file'])
dilate = pe.Node(fsl.DilateImage(operation='mean'), name='dilate')
fast = pe.Node(fsl.FAST(), name='fast')
outputspec = pe.Node(niu.IdentityInterface(fields=[
'mask', 'reg_file', 'segments', 'warped_struct', 'bet_struct',
'inverse_reg'
]),
name='outputspec')
#create brain mask
wf.connect(inputspec, "structural", bet, "in_file")
# calculate transfor, struct --> func
wf.connect(inputspec, "functional", flirt, "reference")
wf.connect(inputspec, "structural", flirt, "in_file")
wf.connect(flirt, 'out_matrix_file', outputspec, 'reg_file')
wf.connect(flirt, 'out_file', outputspec, 'warped_struct')
# Calculate inverse
wf.connect(inputspec, "functional", flirt_inv, "in_file")
wf.connect(inputspec, "structural", flirt_inv, "reference")
wf.connect(flirt_inv, "out_matrix_file", outputspec, "inverse_reg")
#dilate brain mask
wf.connect(bet, "mask_file", dilate, "in_file")
#transform mask to functional space
wf.connect(dilate, "out_file", applyxfm_mask, "in_file")
wf.connect(inputspec, "functional", applyxfm_mask, "reference")
wf.connect(flirt, "out_matrix_file", applyxfm_mask, "in_matrix_file")
wf.connect(applyxfm_mask, 'out_file', outputspec, 'mask')
#segment with FAST
wf.connect(bet, "out_file", fast, "in_files")
wf.connect(bet, "out_file", outputspec, "bet_struct")
#transform segments
wf.connect(fast, "tissue_class_map", applyxfm_seg, "in_file")
wf.connect(flirt, 'out_matrix_file', applyxfm_seg, "in_matrix_file")
wf.connect(inputspec, "functional", applyxfm_seg, "reference")
wf.connect(applyxfm_seg, "out_file", outputspec, "segments")
return wf
def init_enhance_and_skullstrip_dwi_wf(
name="enhance_and_skullstrip_dwi_wf", omp_nthreads=1
):
"""
Enhance a *b0* reference and perform brain extraction.
This workflow takes in a *b0* reference image and sharpens the histogram
with the application of the N4 algorithm for removing the
:abbr:`INU (intensity non-uniformity)` bias field and calculates a signal
mask.
Steps of this workflow are:
1. Run ANTs' ``N4BiasFieldCorrection`` on the input
dwi reference image and mask.
2. Calculate a loose mask using FSL's ``bet``, with one mathematical morphology
dilation of one iteration and a sphere of 6mm as structuring element.
3. Mask the :abbr:`INU (intensity non-uniformity)`-corrected image
with the latest mask calculated in 3), then use AFNI's ``3dUnifize``
to *standardize* the T2* contrast distribution.
4. Calculate a mask using AFNI's ``3dAutomask`` after the contrast
enhancement of 4).
5. Calculate a final mask as the intersection of 2) and 4).
6. Apply final mask on the enhanced reference.
Workflow Graph:
.. workflow ::
:graph2use: orig
:simple_form: yes
from dmriprep.workflows.dwi.util import init_enhance_and_skullstrip_dwi_wf
wf = init_enhance_and_skullstrip_dwi_wf(omp_nthreads=1)
.. _N4BiasFieldCorrection: https://hdl.handle.net/10380/3053
Parameters
----------
name : str
Name of workflow (default: ``enhance_and_skullstrip_dwi_wf``)
omp_nthreads : int
number of threads available to parallel nodes
Inputs
------
in_file
The *b0* reference (single volume)
pre_mask
initial mask
Outputs
-------
bias_corrected_file
the ``in_file`` after `N4BiasFieldCorrection`_
skull_stripped_file
the ``bias_corrected_file`` after skull-stripping
mask_file
mask of the skull-stripped input file
out_report
reportlet for the skull-stripping
"""
from niworkflows.interfaces.header import CopyXForm
from niworkflows.interfaces.fixes import (
FixN4BiasFieldCorrection as N4BiasFieldCorrection,
)
from niworkflows.interfaces.nibabel import ApplyMask
workflow = Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(fields=["in_file", "pre_mask"]), name="inputnode"
)
outputnode = pe.Node(
niu.IdentityInterface(
fields=["mask_file", "skull_stripped_file", "bias_corrected_file"]
),
name="outputnode",
)
# Run N4 normally, force num_threads=1 for stability (images are small, no need for >1)
n4_correct = pe.Node(
N4BiasFieldCorrection(
dimension=3, copy_header=True, bspline_fitting_distance=200
),
shrink_factor=2,
name="n4_correct",
n_procs=1,
)
n4_correct.inputs.rescale_intensities = True
# Create a generous BET mask out of the bias-corrected EPI
skullstrip_first_pass = pe.Node(
fsl.BET(frac=0.2, mask=True), name="skullstrip_first_pass"
)
bet_dilate = pe.Node(
fsl.DilateImage(
operation="max",
kernel_shape="sphere",
kernel_size=6.0,
internal_datatype="char",
),
name="skullstrip_first_dilate",
)
bet_mask = pe.Node(fsl.ApplyMask(), name="skullstrip_first_mask")
# Use AFNI's unifize for T2 contrast & fix header
unifize = pe.Node(
afni.Unifize(
t2=True,
outputtype="NIFTI_GZ",
args="-clfrac 0.2 -rbt 18.3 65.0 90.0",
out_file="uni.nii.gz",
),
name="unifize",
)
fixhdr_unifize = pe.Node(CopyXForm(), name="fixhdr_unifize", mem_gb=0.1)
# Run AFNI's 3dAutomask to extract a refined brain mask
skullstrip_second_pass = pe.Node(
afni.Automask(dilate=1, outputtype="NIFTI_GZ"), name="skullstrip_second_pass"
)
fixhdr_skullstrip2 = pe.Node(CopyXForm(), name="fixhdr_skullstrip2", mem_gb=0.1)
# Take intersection of both masks
combine_masks = pe.Node(fsl.BinaryMaths(operation="mul"), name="combine_masks")
normalize = pe.Node(niu.Function(function=_normalize), name="normalize")
# Compute masked brain
apply_mask = pe.Node(ApplyMask(), name="apply_mask")
# fmt:off
workflow.connect([
(inputnode, n4_correct, [("in_file", "input_image"),
("pre_mask", "mask_image")]),
(inputnode, fixhdr_unifize, [("in_file", "hdr_file")]),
(inputnode, fixhdr_skullstrip2, [("in_file", "hdr_file")]),
(n4_correct, skullstrip_first_pass, [("output_image", "in_file")]),
(skullstrip_first_pass, bet_dilate, [("mask_file", "in_file")]),
(bet_dilate, bet_mask, [("out_file", "mask_file")]),
(skullstrip_first_pass, bet_mask, [("out_file", "in_file")]),
(bet_mask, unifize, [("out_file", "in_file")]),
(unifize, fixhdr_unifize, [("out_file", "in_file")]),
(fixhdr_unifize, skullstrip_second_pass, [("out_file", "in_file")]),
(skullstrip_first_pass, combine_masks, [("mask_file", "in_file")]),
(skullstrip_second_pass, fixhdr_skullstrip2, [("out_file", "in_file")]),
(fixhdr_skullstrip2, combine_masks, [("out_file", "operand_file")]),
(combine_masks, apply_mask, [("out_file", "in_mask")]),
(combine_masks, outputnode, [("out_file", "mask_file")]),
(n4_correct, normalize, [("output_image", "in_file")]),
(normalize, apply_mask, [("out", "in_file")]),
(normalize, outputnode, [("out", "bias_corrected_file")]),
(apply_mask, outputnode, [("out_file", "skull_stripped_file")]),
]
)
# fmt:on
return workflow
def init_enhance_and_skullstrip_bold_wf(
brainmask_thresh=0.5,
name="enhance_and_skullstrip_bold_wf",
omp_nthreads=1,
pre_mask=False,
):
"""
Enhance and run brain extraction on a BOLD EPI image.
This workflow takes in a :abbr:`BOLD (blood-oxygen level-dependant)`
:abbr:`fMRI (functional MRI)` average/summary (e.g., a reference image
averaging non-steady-state timepoints), and sharpens the histogram
with the application of the N4 algorithm for removing the
:abbr:`INU (intensity non-uniformity)` bias field and calculates a signal
mask.
Steps of this workflow are:
1. Calculate a tentative mask by registering (9-parameters) to *fMRIPrep*'s
:abbr:`EPI (echo-planar imaging)` -*boldref* template, which
is in MNI space.
The tentative mask is obtained by resampling the MNI template's
brainmask into *boldref*-space.
2. Binary dilation of the tentative mask with a sphere of 3mm diameter.
3. Run ANTs' ``N4BiasFieldCorrection`` on the input
:abbr:`BOLD (blood-oxygen level-dependant)` average, using the
mask generated in 1) instead of the internal Otsu thresholding.
4. Calculate a loose mask using FSL's ``bet``, with one mathematical morphology
dilation of one iteration and a sphere of 6mm as structuring element.
5. Mask the :abbr:`INU (intensity non-uniformity)`-corrected image
with the latest mask calculated in 3), then use AFNI's ``3dUnifize``
to *standardize* the T2* contrast distribution.
6. Calculate a mask using AFNI's ``3dAutomask`` after the contrast
enhancement of 4).
7. Calculate a final mask as the intersection of 4) and 6).
8. Apply final mask on the enhanced reference.
Step 1 can be skipped if the ``pre_mask`` argument is set to ``True`` and
a tentative mask is passed in to the workflow throught the ``pre_mask``
Nipype input.
Workflow graph
.. workflow ::
:graph2use: orig
:simple_form: yes
from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf
wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=1)
.. _N4BiasFieldCorrection: https://hdl.handle.net/10380/3053
Parameters
----------
brainmask_thresh: :obj:`float`
Lower threshold for the probabilistic brainmask to obtain
the final binary mask (default: 0.5).
name : str
Name of workflow (default: ``enhance_and_skullstrip_bold_wf``)
omp_nthreads : int
number of threads available to parallel nodes
pre_mask : bool
Indicates whether the ``pre_mask`` input will be set (and thus, step 1
should be skipped).
Inputs
------
in_file : str
BOLD image (single volume)
pre_mask : bool
A tentative brain mask to initialize the workflow (requires ``pre_mask``
parameter set ``True``).
Outputs
-------
bias_corrected_file : str
the ``in_file`` after `N4BiasFieldCorrection`_
skull_stripped_file : str
the ``bias_corrected_file`` after skull-stripping
mask_file : str
mask of the skull-stripped input file
out_report : str
reportlet for the skull-stripping
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=["in_file", "pre_mask"]),
name="inputnode")
outputnode = pe.Node(
niu.IdentityInterface(
fields=["mask_file", "skull_stripped_file", "bias_corrected_file"
]),
name="outputnode",
)
# Dilate pre_mask
pre_dilate = pe.Node(
fsl.DilateImage(
operation="max",
kernel_shape="sphere",
kernel_size=3.0,
internal_datatype="char",
),
name="pre_mask_dilate",
)
# Ensure mask's header matches reference's
check_hdr = pe.Node(MatchHeader(),
name="check_hdr",
run_without_submitting=True)
# Run N4 normally, force num_threads=1 for stability (images are small, no need for >1)
n4_correct = pe.Node(
N4BiasFieldCorrection(dimension=3,
copy_header=True,
bspline_fitting_distance=200),
shrink_factor=2,
name="n4_correct",
n_procs=1,
)
n4_correct.inputs.rescale_intensities = True
# Create a generous BET mask out of the bias-corrected EPI
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2, mask=True),
name="skullstrip_first_pass")
bet_dilate = pe.Node(
fsl.DilateImage(
operation="max",
kernel_shape="sphere",
kernel_size=6.0,
internal_datatype="char",
),
name="skullstrip_first_dilate",
)
bet_mask = pe.Node(fsl.ApplyMask(), name="skullstrip_first_mask")
# Use AFNI's unifize for T2 constrast & fix header
unifize = pe.Node(
afni.Unifize(
t2=True,
outputtype="NIFTI_GZ",
# Default -clfrac is 0.1, 0.4 was too conservative
# -rbt because I'm a Jedi AFNI Master (see 3dUnifize's documentation)
args="-clfrac 0.2 -rbt 18.3 65.0 90.0",
out_file="uni.nii.gz",
),
name="unifize",
)
fixhdr_unifize = pe.Node(CopyXForm(), name="fixhdr_unifize", mem_gb=0.1)
# Run ANFI's 3dAutomask to extract a refined brain mask
skullstrip_second_pass = pe.Node(afni.Automask(dilate=1,
outputtype="NIFTI_GZ"),
name="skullstrip_second_pass")
fixhdr_skullstrip2 = pe.Node(CopyXForm(),
name="fixhdr_skullstrip2",
mem_gb=0.1)
# Take intersection of both masks
combine_masks = pe.Node(fsl.BinaryMaths(operation="mul"),
name="combine_masks")
# Compute masked brain
apply_mask = pe.Node(fsl.ApplyMask(), name="apply_mask")
if not pre_mask:
from ..interfaces.nibabel import Binarize
bold_template = get_template("MNI152NLin2009cAsym",
resolution=2,
desc="fMRIPrep",
suffix="boldref")
brain_mask = get_template("MNI152NLin2009cAsym",
resolution=2,
desc="brain",
suffix="mask")
# Initialize transforms with antsAI
init_aff = pe.Node(
AI(
fixed_image=str(bold_template),
fixed_image_mask=str(brain_mask),
metric=("Mattes", 32, "Regular", 0.2),
transform=("Affine", 0.1),
search_factor=(20, 0.12),
principal_axes=False,
convergence=(10, 1e-6, 10),
verbose=True,
),
name="init_aff",
n_procs=omp_nthreads,
)
# Registration().version may be None
if parseversion(Registration().version or "0.0.0") > Version("2.2.0"):
init_aff.inputs.search_grid = (40, (0, 40, 40))
# Set up spatial normalization
norm = pe.Node(
Registration(from_file=pkgr_fn("niworkflows.data",
"epi_atlasbased_brainmask.json")),
name="norm",
n_procs=omp_nthreads,
)
norm.inputs.fixed_image = str(bold_template)
map_brainmask = pe.Node(
ApplyTransforms(
interpolation="BSpline",
float=True,
# Use the higher resolution and probseg for numerical stability in rounding
input_image=str(
get_template(
"MNI152NLin2009cAsym",
resolution=1,
label="brain",
suffix="probseg",
)),
),
name="map_brainmask",
)
binarize_mask = pe.Node(Binarize(thresh_low=brainmask_thresh),
name="binarize_mask")
# fmt: off
workflow.connect([
(inputnode, init_aff, [("in_file", "moving_image")]),
(inputnode, map_brainmask, [("in_file", "reference_image")]),
(inputnode, norm, [("in_file", "moving_image")]),
(init_aff, norm, [("output_transform", "initial_moving_transform")
]),
(norm, map_brainmask, [
("reverse_invert_flags", "invert_transform_flags"),
("reverse_transforms", "transforms"),
]),
(map_brainmask, binarize_mask, [("output_image", "in_file")]),
(binarize_mask, pre_dilate, [("out_mask", "in_file")]),
])
# fmt: on
else:
# fmt: off
workflow.connect([
(inputnode, pre_dilate, [("pre_mask", "in_file")]),
])
# fmt: on
# fmt: off
workflow.connect([
(inputnode, check_hdr, [("in_file", "reference")]),
(pre_dilate, check_hdr, [("out_file", "in_file")]),
(check_hdr, n4_correct, [("out_file", "mask_image")]),
(inputnode, n4_correct, [("in_file", "input_image")]),
(inputnode, fixhdr_unifize, [("in_file", "hdr_file")]),
(inputnode, fixhdr_skullstrip2, [("in_file", "hdr_file")]),
(n4_correct, skullstrip_first_pass, [("output_image", "in_file")]),
(skullstrip_first_pass, bet_dilate, [("mask_file", "in_file")]),
(bet_dilate, bet_mask, [("out_file", "mask_file")]),
(skullstrip_first_pass, bet_mask, [("out_file", "in_file")]),
(bet_mask, unifize, [("out_file", "in_file")]),
(unifize, fixhdr_unifize, [("out_file", "in_file")]),
(fixhdr_unifize, skullstrip_second_pass, [("out_file", "in_file")]),
(skullstrip_first_pass, combine_masks, [("mask_file", "in_file")]),
(skullstrip_second_pass, fixhdr_skullstrip2, [("out_file", "in_file")
]),
(fixhdr_skullstrip2, combine_masks, [("out_file", "operand_file")]),
(fixhdr_unifize, apply_mask, [("out_file", "in_file")]),
(combine_masks, apply_mask, [("out_file", "mask_file")]),
(combine_masks, outputnode, [("out_file", "mask_file")]),
(apply_mask, outputnode, [("out_file", "skull_stripped_file")]),
(n4_correct, outputnode, [("output_image", "bias_corrected_file")]),
])
# fmt: on
return workflow
def init_enhance_and_skullstrip_asl_wf(
brainmask_thresh=0.5,
name="enhance_and_skullstrip_asl_wf",
omp_nthreads=1,
pre_mask=False,
):
"""
Enhance and run brain extraction on a ASL image.
This workflow takes in a :abbr:`ASL (Aretrrail Spin Labeling)`
average/summary (e.g., a reference image
averaging non-steady-state timepoints), and sharpens the histogram
with the application of the N4 algorithm for removing the
:abbr:`INU (intensity non-uniformity)` bias field and calculates a signal
mask.
Steps of this workflow are:
1. Calculate a tentative mask by registering (9-parameters) to *fMRIPrep*'s
:abbr:`EPI (echo-planar imaging)` -*aslref* template, which
is in MNI space.
The tentative mask is obtained by resampling the MNI template's
brainmask into *aslref*-space.
2. Binary dilation of the tentative mask with a sphere of 3mm diameter.
3. Run ANTs' ``N4BiasFieldCorrection`` on the input
:abbr:`ASL (arterial spin labeling)` average, using the
mask generated in 1) instead of the internal Otsu thresholding.
4. Calculate a loose mask using FSL's ``bet``, with one mathematical morphology
dilation of one iteration and a sphere of 6mm as structuring element.
5. Mask the :abbr:`INU (intensity non-uniformity)`-corrected image
with the latest mask calculated in 3), then use AFNI's ``3dUnifize``
to *standardize* the T2* contrast distribution.
6. Calculate a mask using AFNI's ``3dAutomask`` after the contrast
enhancement of 4).
7. Calculate a final mask as the intersection of 4) and 6).
8. Apply final mask on the enhanced reference.
Step 1 can be skipped if the ``pre_mask`` argument is set to ``True`` and
a tentative mask is passed in to the workflow throught the ``pre_mask``
Nipype input.
Workflow graph
.. workflow ::
:graph2use: orig
:simple_form: yes
from niworkflows.func.util import init_enhance_and_skullstrip_asl_wf
wf = init_enhance_and_skullstrip_asl_wf(omp_nthreads=1)
.. _N4BiasFieldCorrection: https://hdl.handle.net/10380/3053
Parameters
----------
brainmask_thresh: :obj:`float`
Lower threshold for the probabilistic brainmask to obtain
the final binary mask (default: 0.5).
name : str
Name of workflow (default: ``enhance_and_skullstrip_asl_wf``)
omp_nthreads : int
number of threads available to parallel nodes
pre_mask : bool
Indicates whether the ``pre_mask`` input will be set (and thus, step 1
should be skipped).
Inputs
------
in_file : str
ASL image (single volume)
pre_mask : bool
A tentative brain mask to initialize the workflow (requires ``pre_mask``
parameter set ``True``).
Outputs
-------
bias_corrected_file : str
the ``in_file`` after `N4BiasFieldCorrection`_
skull_stripped_file : str
the ``bias_corrected_file`` after skull-stripping
mask_file : str
mask of the skull-stripped input file
out_report : str
reportlet for the skull-stripping
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=["in_file", "pre_mask"]),
name="inputnode")
outputnode = pe.Node(
niu.IdentityInterface(
fields=["mask_file", "skull_stripped_file", "bias_corrected_file"
]),
name="outputnode",
)
pre_mask = pre_mask
# Ensure mask's header matches reference's
#check_hdr = pe.Node(MatchHeader(), name="check_hdr", run_without_submitting=True)
# Run N4 normally, force num_threads=1 for stability (images are small, no need for >1)
n4_correct = pe.Node(
N4BiasFieldCorrection(dimension=3,
copy_header=True,
bspline_fitting_distance=200),
shrink_factor=2,
name="n4_correct",
n_procs=1,
)
n4_correct.inputs.rescale_intensities = True
# Create a generous BET mask out of the bias-corrected EPI
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2, mask=True),
name="skullstrip_first_pass")
bet_dilate = pe.Node(
fsl.DilateImage(
operation="max",
kernel_shape="sphere",
kernel_size=6.0,
internal_datatype="char",
),
name="skullstrip_first_dilate",
)
bet_mask = pe.Node(fsl.ApplyMask(), name="skullstrip_first_mask")
# Use AFNI's unifize for T2 constrast & fix header
unifize = pe.Node(
afni.Unifize(
t2=True,
outputtype="NIFTI_GZ",
# Default -clfrac is 0.1, 0.4 was too conservative
# -rbt because I'm a Jedi AFNI Master (see 3dUnifize's documentation)
args="-clfrac 0.2 -rbt 18.3 65.0 90.0",
out_file="uni.nii.gz",
),
name="unifize",
)
fixhdr_unifize = pe.Node(CopyXForm(), name="fixhdr_unifize", mem_gb=0.1)
# Run ANFI's 3dAutomask to extract a refined brain mask
skullstrip_second_pass = pe.Node(afni.Automask(dilate=1,
outputtype="NIFTI_GZ"),
name="skullstrip_second_pass")
fixhdr_skullstrip2 = pe.Node(CopyXForm(),
name="fixhdr_skullstrip2",
mem_gb=0.1)
# Take intersection of both masks
combine_masks = pe.Node(fsl.BinaryMaths(operation="mul"),
name="combine_masks")
# Compute masked brain
apply_mask = pe.Node(fsl.ApplyMask(), name="apply_mask")
#binarize_mask = pe.Node(Binarize(thresh_low=brainmask_thresh), name="binarize_mask")
# fmt: off
workflow.connect([
(inputnode, n4_correct, [("in_file", "mask_image")]),
(inputnode, n4_correct, [("in_file", "input_image")]),
(inputnode, fixhdr_unifize, [("in_file", "hdr_file")]),
(inputnode, fixhdr_skullstrip2, [("in_file", "hdr_file")]),
(n4_correct, skullstrip_first_pass, [("output_image", "in_file")]),
(skullstrip_first_pass, bet_dilate, [("mask_file", "in_file")]),
(bet_dilate, bet_mask, [("out_file", "mask_file")]),
(skullstrip_first_pass, bet_mask, [("out_file", "in_file")]),
(bet_mask, unifize, [("out_file", "in_file")]),
(unifize, fixhdr_unifize, [("out_file", "in_file")]),
(fixhdr_unifize, skullstrip_second_pass, [("out_file", "in_file")]),
(skullstrip_first_pass, combine_masks, [("mask_file", "in_file")]),
(skullstrip_second_pass, fixhdr_skullstrip2, [("out_file", "in_file")
]),
(fixhdr_skullstrip2, combine_masks, [("out_file", "operand_file")]),
(fixhdr_unifize, apply_mask, [("out_file", "in_file")]),
(combine_masks, apply_mask, [("out_file", "mask_file")]),
(combine_masks, outputnode, [("out_file", "mask_file")]),
(apply_mask, outputnode, [("out_file", "skull_stripped_file")]),
(n4_correct, outputnode, [("output_image", "bias_corrected_file")]),
])
# fmt: on
return workflow
def t1_freesurfer_pipeline(name='t1_preproc', use_T2=False):
inputnode = pe.Node(utility.IdentityInterface(
fields=['t1_files', 't2_file', 'subject_id']),
run_without_submitting=True,
name='inputspec')
n_freesurfer = pe.Node(
interface=freesurfer.ReconAll(directive='all', use_T2=use_T2),
name='freesurfer',
)
n_fs_seg2mask = pe.Node(utility.Function(
input_names=['parc_file', 'out_file'],
output_names=['out_file'],
function=fs_seg2mask),
name='fs_seg2mask')
n_fs_seg2mask.inputs.out_file = 'mask.nii'
n_autobox_mask_fs = pe.Node(afni.Autobox(padding=15,
out_file='%s_crop.nii'),
name='autobox_mask_fs')
n_compute_pvmaps = pe.Node(freesurfer.utils.ComputeVolumeFractions(
gm_file='pve.nii.gz',
niigz=True,
),
name='compute_pvmaps')
n_crop_t1 = pe.Node(nipy.Crop(out_file='%s_crop.nii.gz',
outputtype='NIFTI_GZ'),
name='crop_t1')
n_crop_brain = pe.Node(nipy.Crop(out_file='%s_crop.nii.gz',
outputtype='NIFTI_GZ'),
name='crop_brain')
n_t1_nii = pe.Node(freesurfer.MRIConvert(out_type='niigz'), name='t1_nii')
n_dilate_mask = pe.Node(fsl.DilateImage(operation='mean',
kernel_shape='3D'),
name='dilate_mask')
n_reg_crop = pe.Node(freesurfer.Tkregister(reg_file='reg_crop.dat',
freeview='freeview.mat',
fsl_reg_out='fsl_reg_out.mat',
lta_out='lta.mat',
xfm_out='xfm.mat',
reg_header=True),
name='reg_crop')
w = pe.Workflow(name=name)
if (use_T2):
w.connect([(inputnode, n_freesurfer, [
('t2_file', 'T2_file'),
])])
w.connect([
(inputnode, n_freesurfer, [('t1_files', 'T1_files'),
('subject_id', 'subject_id')]),
(n_freesurfer, n_fs_seg2mask, [(('aparc_aseg', utility.select, 1),
'parc_file')]),
(n_fs_seg2mask, n_autobox_mask_fs, [('out_file', 'in_file')]),
(n_autobox_mask_fs, n_dilate_mask, [('out_file', 'in_file')]),
(n_autobox_mask_fs, n_crop_t1, [('%s_min' % c, ) * 2 for c in 'xyz'] +
[(('%s_max' % c, wrap(operator.__add__), [1]), '%s_max' % c)
for c in 'xyz']), # add 1 for boundary inclusive
(n_freesurfer, n_crop_t1, [('T1', 'in_file')]),
(n_autobox_mask_fs, n_crop_brain, [('%s_min' % c, ) * 2
for c in 'xyz'] +
[(('%s_max' % c, wrap(operator.__add__), [1]), '%s_max' % c)
for c in 'xyz']), # add 1 for boundary inclusive
(n_freesurfer, n_crop_brain, [('norm', 'in_file')]),
(n_freesurfer, n_t1_nii, [('T1', 'in_file')]),
(n_freesurfer, n_reg_crop, [('norm', 'target'), ('subject_id', ) * 2,
('subjects_dir', ) * 2]),
(n_autobox_mask_fs, n_reg_crop, [('out_file', 'mov')]),
(n_reg_crop, n_compute_pvmaps, [('reg_file', ) * 2]),
(n_autobox_mask_fs, n_compute_pvmaps, [('out_file', 'in_file')]),
(n_freesurfer, n_compute_pvmaps, [('subjects_dir', ) * 2])
])
return w
def create_old_segment_pipe(params_template, params={},
name="old_segment_pipe"):
"""
Description: Extract brain using tissues masks output by SPM's old_segment
function:
- Segment the T1 using given priors;
- Threshold GM, WM and CSF maps;
- Compute union of those 3 tissues;
- Apply morphological opening on the union mask
- Fill holes
Inputs:
inputnode:
T1: T1 file name
arguments:
priors: list of file names
params: dictionary of node sub-parameters (from a json file)
name: pipeline name (default = "old_segment_pipe")
Outputs:
fill_holes.out_file:
filled mask after erode
fill_holes_dil.out_file
filled mask after dilate
threshold_gm, threshold_wm, threshold_csf.out_file:
resp grey matter, white matter, and csf after thresholding
"""
# creating pipeline
be_pipe = pe.Workflow(name=name)
# Creating inputnode
inputnode = pe.Node(
niu.IdentityInterface(fields=['T1', 'indiv_params']),
name='inputnode'
)
# Segment in to 6 tissues
segment = NodeParams(spm.Segment(),
params=parse_key(params, "segment"),
name="old_segment")
segment.inputs.tissue_prob_maps = [params_template["template_gm"],
params_template["template_wm"],
params_template["template_csf"]]
be_pipe.connect(inputnode, 'T1', segment, 'data')
# Threshold GM, WM and CSF
thd_nodes = {}
for tissue in ['gm', 'wm', 'csf']:
tmp_node = NodeParams(fsl.Threshold(),
params=parse_key(params, "threshold_" + tissue),
name="threshold_" + tissue)
be_pipe.connect(segment, 'native_' + tissue + '_image',
tmp_node, 'in_file')
be_pipe.connect(
inputnode, ('indiv_params', parse_key, "threshold_" + tissue),
tmp_node, "indiv_params")
thd_nodes[tissue] = tmp_node
# Compute union of the 3 tissues
# Done with 2 fslmaths as it seems to hard to do it
wmgm_union = pe.Node(fsl.BinaryMaths(), name="wmgm_union")
wmgm_union.inputs.operation = "add"
be_pipe.connect(thd_nodes['gm'], 'out_file', wmgm_union, 'in_file')
be_pipe.connect(thd_nodes['wm'], 'out_file', wmgm_union, 'operand_file')
tissues_union = pe.Node(fsl.BinaryMaths(), name="tissues_union")
tissues_union.inputs.operation = "add"
be_pipe.connect(wmgm_union, 'out_file', tissues_union, 'in_file')
be_pipe.connect(thd_nodes['csf'], 'out_file',
tissues_union, 'operand_file')
# Opening
dilate_mask = NodeParams(fsl.DilateImage(),
params=parse_key(params, "dilate_mask"),
name="dilate_mask")
dilate_mask.inputs.operation = "mean" # Arbitrary operation
be_pipe.connect(tissues_union, 'out_file', dilate_mask, 'in_file')
# Eroding mask
erode_mask = NodeParams(fsl.ErodeImage(),
params=parse_key(params, "erode_mask"),
name="erode_mask")
be_pipe.connect(tissues_union, 'out_file', erode_mask, 'in_file')
# fill holes of erode_mask
fill_holes = pe.Node(BinaryFillHoles(), name="fill_holes")
be_pipe.connect(erode_mask, 'out_file', fill_holes, 'in_file')
# fill holes of dilate_mask
fill_holes_dil = pe.Node(BinaryFillHoles(), name="fill_holes_dil")
be_pipe.connect(dilate_mask, 'out_file', fill_holes_dil, 'in_file')
return be_pipe
def skullstrip_functional(tool='afni', wf_name='skullstrip_functional'):
tool = tool.lower()
if tool != 'afni' and tool != 'fsl' and tool != 'fsl_afni':
raise Exception("\n\n[!] Error: The 'tool' parameter of the "
"'skullstrip_functional' workflow must be either "
"'afni' or 'fsl'.\n\nTool input: "
"{0}\n\n".format(tool))
wf = pe.Workflow(name=wf_name)
input_node = pe.Node(util.IdentityInterface(fields=['func']),
name='inputspec')
output_node = pe.Node(
util.IdentityInterface(fields=['func_brain', 'func_brain_mask']),
name='outputspec')
if tool == 'afni':
func_get_brain_mask = pe.Node(interface=preprocess.Automask(),
name='func_get_brain_mask_AFNI')
func_get_brain_mask.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'func', func_get_brain_mask, 'in_file')
wf.connect(func_get_brain_mask, 'out_file', output_node,
'func_brain_mask')
elif tool == 'fsl':
func_get_brain_mask = pe.Node(interface=fsl.BET(),
name='func_get_brain_mask_BET')
func_get_brain_mask.inputs.mask = True
func_get_brain_mask.inputs.functional = True
erode_one_voxel = pe.Node(interface=fsl.ErodeImage(),
name='erode_one_voxel')
erode_one_voxel.inputs.kernel_shape = 'box'
erode_one_voxel.inputs.kernel_size = 1.0
wf.connect(input_node, 'func', func_get_brain_mask, 'in_file')
wf.connect(func_get_brain_mask, 'mask_file', erode_one_voxel,
'in_file')
wf.connect(erode_one_voxel, 'out_file', output_node, 'func_brain_mask')
elif tool == 'fsl_afni':
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2,
mask=True,
functional=True),
name='skullstrip_first_pass')
bet_dilate = pe.Node(fsl.DilateImage(operation='max',
kernel_shape='sphere',
kernel_size=6.0,
internal_datatype='char'),
name='skullstrip_first_dilate')
bet_mask = pe.Node(fsl.ApplyMask(), name='skullstrip_first_mask')
unifize = pe.Node(afni_utils.Unifize(
t2=True,
outputtype='NIFTI_GZ',
args='-clfrac 0.2 -rbt 18.3 65.0 90.0',
out_file="uni.nii.gz"),
name='unifize')
skullstrip_second_pass = pe.Node(preprocess.Automask(
dilate=1, outputtype='NIFTI_GZ'),
name='skullstrip_second_pass')
combine_masks = pe.Node(fsl.BinaryMaths(operation='mul'),
name='combine_masks')
wf.connect([
(input_node, skullstrip_first_pass, [('func', 'in_file')]),
(skullstrip_first_pass, bet_dilate, [('mask_file', 'in_file')]),
(bet_dilate, bet_mask, [('out_file', 'mask_file')]),
(skullstrip_first_pass, bet_mask, [('out_file', 'in_file')]),
(bet_mask, unifize, [('out_file', 'in_file')]),
(unifize, skullstrip_second_pass, [('out_file', 'in_file')]),
(skullstrip_first_pass, combine_masks, [('mask_file', 'in_file')]),
(skullstrip_second_pass, combine_masks, [('out_file',
'operand_file')]),
(combine_masks, output_node, [('out_file', 'func_brain_mask')])
])
func_edge_detect = pe.Node(interface=afni_utils.Calc(),
name='func_extract_brain')
func_edge_detect.inputs.expr = 'a*b'
func_edge_detect.inputs.outputtype = 'NIFTI_GZ'
wf.connect(input_node, 'func', func_edge_detect, 'in_file_a')
if tool == 'afni':
wf.connect(func_get_brain_mask, 'out_file', func_edge_detect,
'in_file_b')
elif tool == 'fsl':
wf.connect(erode_one_voxel, 'out_file', func_edge_detect, 'in_file_b')
elif tool == 'fsl_afni':
wf.connect(combine_masks, 'out_file', func_edge_detect, 'in_file_b')
wf.connect(func_edge_detect, 'out_file', output_node, 'func_brain')
return wf
def init_enhance_and_skullstrip_bold_wf(name='enhance_and_skullstrip_bold_wf',
pre_mask=False,
omp_nthreads=1):
"""
This workflow takes in a :abbr:`BOLD (blood-oxygen level-dependant)`
:abbr:`fMRI (functional MRI)` average/summary (e.g., a reference image
averaging non-steady-state timepoints), and sharpens the histogram
with the application of the N4 algorithm for removing the
:abbr:`INU (intensity non-uniformity)` bias field and calculates a signal
mask.
Steps of this workflow are:
1. Calculate a tentative mask by registering (9-parameters) to *fMRIPrep*'s
:abbr:`EPI (echo-planar imaging)` -*boldref* template, which
is in MNI space.
The tentative mask is obtained by resampling the MNI template's
brainmask into *boldref*-space.
2. Binary dilation of the tentative mask with a sphere of 3mm diameter.
3. Run ANTs' ``N4BiasFieldCorrection`` on the input
:abbr:`BOLD (blood-oxygen level-dependant)` average, using the
mask generated in 1) instead of the internal Otsu thresholding.
4. Calculate a loose mask using FSL's ``bet``, with one mathematical morphology
dilation of one iteration and a sphere of 6mm as structuring element.
5. Mask the :abbr:`INU (intensity non-uniformity)`-corrected image
with the latest mask calculated in 3), then use AFNI's ``3dUnifize``
to *standardize* the T2* contrast distribution.
6. Calculate a mask using AFNI's ``3dAutomask`` after the contrast
enhancement of 4).
7. Calculate a final mask as the intersection of 4) and 6).
8. Apply final mask on the enhanced reference.
Step 1 can be skipped if the ``pre_mask`` argument is set to ``True`` and
a tentative mask is passed in to the workflow throught the ``pre_mask``
Nipype input.
.. workflow ::
:graph2use: orig
:simple_form: yes
from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf
wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=1)
**Parameters**
name : str
Name of workflow (default: ``enhance_and_skullstrip_bold_wf``)
pre_mask : bool
Indicates whether the ``pre_mask`` input will be set (and thus, step 1
should be skipped).
omp_nthreads : int
number of threads available to parallel nodes
**Inputs**
in_file
BOLD image (single volume)
pre_mask : bool
A tentative brain mask to initialize the workflow (requires ``pre_mask``
parameter set ``True``).
**Outputs**
bias_corrected_file
the ``in_file`` after `N4BiasFieldCorrection`_
skull_stripped_file
the ``bias_corrected_file`` after skull-stripping
mask_file
mask of the skull-stripped input file
out_report
reportlet for the skull-stripping
.. _N4BiasFieldCorrection: https://hdl.handle.net/10380/3053
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file', 'pre_mask']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['mask_file', 'skull_stripped_file', 'bias_corrected_file']),
name='outputnode')
# Dilate pre_mask
pre_dilate = pe.Node(fsl.DilateImage(operation='max',
kernel_shape='sphere',
kernel_size=3.0,
internal_datatype='char'),
name='pre_mask_dilate')
# Ensure mask's header matches reference's
check_hdr = pe.Node(MatchHeader(),
name='check_hdr',
run_without_submitting=True)
# Run N4 normally, force num_threads=1 for stability (images are small, no need for >1)
n4_correct = pe.Node(ants.N4BiasFieldCorrection(
dimension=3, copy_header=True, bspline_fitting_distance=200),
name='n4_correct',
n_procs=1)
# Create a generous BET mask out of the bias-corrected EPI
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2, mask=True),
name='skullstrip_first_pass')
bet_dilate = pe.Node(fsl.DilateImage(operation='max',
kernel_shape='sphere',
kernel_size=6.0,
internal_datatype='char'),
name='skullstrip_first_dilate')
bet_mask = pe.Node(fsl.ApplyMask(), name='skullstrip_first_mask')
# Use AFNI's unifize for T2 constrast & fix header
unifize = pe.Node(
afni.Unifize(
t2=True,
outputtype='NIFTI_GZ',
# Default -clfrac is 0.1, 0.4 was too conservative
# -rbt because I'm a Jedi AFNI Master (see 3dUnifize's documentation)
args='-clfrac 0.2 -rbt 18.3 65.0 90.0',
out_file="uni.nii.gz"),
name='unifize')
fixhdr_unifize = pe.Node(CopyXForm(), name='fixhdr_unifize', mem_gb=0.1)
# Run ANFI's 3dAutomask to extract a refined brain mask
skullstrip_second_pass = pe.Node(afni.Automask(dilate=1,
outputtype='NIFTI_GZ'),
name='skullstrip_second_pass')
fixhdr_skullstrip2 = pe.Node(CopyXForm(),
name='fixhdr_skullstrip2',
mem_gb=0.1)
# Take intersection of both masks
combine_masks = pe.Node(fsl.BinaryMaths(operation='mul'),
name='combine_masks')
# Compute masked brain
apply_mask = pe.Node(fsl.ApplyMask(), name='apply_mask')
if not pre_mask:
bold_template = get_template('MNI152NLin2009cAsym',
resolution=2,
desc='fMRIPrep',
suffix='boldref')
brain_mask = get_template('MNI152NLin2009cAsym',
resolution=2,
desc='brain',
suffix='mask')
# Initialize transforms with antsAI
init_aff = pe.Node(AI(fixed_image=str(bold_template),
fixed_image_mask=str(brain_mask),
metric=('Mattes', 32, 'Regular', 0.2),
transform=('Affine', 0.1),
search_factor=(20, 0.12),
principal_axes=False,
convergence=(10, 1e-6, 10),
verbose=True),
name='init_aff',
n_procs=omp_nthreads)
# Registration().version may be None
if parseversion(Registration().version or '0.0.0') > Version('2.2.0'):
init_aff.inputs.search_grid = (40, (0, 40, 40))
# Set up spatial normalization
norm = pe.Node(Registration(from_file=pkgr_fn(
'fmriprep.data', 'epi_atlasbased_brainmask.json')),
name='norm',
n_procs=omp_nthreads)
norm.inputs.fixed_image = str(bold_template)
map_brainmask = pe.Node(ApplyTransforms(interpolation='MultiLabel',
float=True,
input_image=str(brain_mask)),
name='map_brainmask')
workflow.connect([
(inputnode, init_aff, [('in_file', 'moving_image')]),
(inputnode, map_brainmask, [('in_file', 'reference_image')]),
(inputnode, norm, [('in_file', 'moving_image')]),
(init_aff, norm, [('output_transform', 'initial_moving_transform')
]),
(norm, map_brainmask, [('reverse_invert_flags',
'invert_transform_flags'),
('reverse_transforms', 'transforms')]),
(map_brainmask, pre_dilate, [('output_image', 'in_file')]),
])
else:
workflow.connect([
(inputnode, pre_dilate, [('pre_mask', 'in_file')]),
])
workflow.connect([
(inputnode, check_hdr, [('in_file', 'reference')]),
(pre_dilate, check_hdr, [('out_file', 'in_file')]),
(check_hdr, n4_correct, [('out_file', 'mask_image')]),
(inputnode, n4_correct, [('in_file', 'input_image')]),
(inputnode, fixhdr_unifize, [('in_file', 'hdr_file')]),
(inputnode, fixhdr_skullstrip2, [('in_file', 'hdr_file')]),
(n4_correct, skullstrip_first_pass, [('output_image', 'in_file')]),
(skullstrip_first_pass, bet_dilate, [('mask_file', 'in_file')]),
(bet_dilate, bet_mask, [('out_file', 'mask_file')]),
(skullstrip_first_pass, bet_mask, [('out_file', 'in_file')]),
(bet_mask, unifize, [('out_file', 'in_file')]),
(unifize, fixhdr_unifize, [('out_file', 'in_file')]),
(fixhdr_unifize, skullstrip_second_pass, [('out_file', 'in_file')]),
(skullstrip_first_pass, combine_masks, [('mask_file', 'in_file')]),
(skullstrip_second_pass, fixhdr_skullstrip2, [('out_file', 'in_file')
]),
(fixhdr_skullstrip2, combine_masks, [('out_file', 'operand_file')]),
(fixhdr_unifize, apply_mask, [('out_file', 'in_file')]),
(combine_masks, apply_mask, [('out_file', 'mask_file')]),
(combine_masks, outputnode, [('out_file', 'mask_file')]),
(apply_mask, outputnode, [('out_file', 'skull_stripped_file')]),
(n4_correct, outputnode, [('output_image', 'bias_corrected_file')]),
])
return workflow
def prepare_template_wf(name="prepare_template"):
wf = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['tpl_t1w', 'tpl_t1w_brainmask', 'CSF_pve']),
name='inputnode')
tpl_t1w_brain = pe.Node(fsl.ApplyMask(), name='tpl_t1w_brain')
wf.connect(inputnode, "tpl_t1w", tpl_t1w_brain, "in_file")
wf.connect(inputnode, "tpl_t1w_brainmask", tpl_t1w_brain, "mask_file")
norm_wf = get_norm_wf()
wf.connect(inputnode, 'tpl_t1w', norm_wf, "inputnode.t1w")
wf.connect(tpl_t1w_brain, 'out_file', norm_wf, "inputnode.t1w_brain")
MNI_2_t1w_warp = pe.Node(fsl.InvWarp(), name='MNI_2_t1w_warp')
wf.connect(inputnode, 'tpl_t1w', MNI_2_t1w_warp, 'reference')
wf.connect(norm_wf, 'outputnode.t1w_2_MNI_warp', MNI_2_t1w_warp, 'warp')
bianca_mask = pe.Node(MakeBiancaMask(), name='bianca_mask')
bianca_mask.inputs.keep_intermediate_files = 0
wf.connect(inputnode, 'tpl_t1w', bianca_mask, 'structural_image')
wf.connect(inputnode, 'CSF_pve', bianca_mask, 'CSF_pve')
wf.connect(MNI_2_t1w_warp, 'inverse_warp', bianca_mask,
'warp_file_MNI2structural')
wf.connect(tpl_t1w_brain, 'out_file', bianca_mask,
'structural_image_brainextracted')
wf.connect(inputnode, 'tpl_t1w_brainmask', bianca_mask, 'brainmask')
# distancemap
# dilate for distancemap to avoid rim effects when resampling distancemap
brainmask_dil = pe.Node(fsl.DilateImage(operation="max"),
name="brainmask_dil")
wf.connect(inputnode, 'tpl_t1w_brainmask', brainmask_dil, "in_file")
distancemap = pe.Node(fsl.DistanceMap(), name="distancemap")
wf.connect(bianca_mask, 'vent_file', distancemap, "in_file")
wf.connect(brainmask_dil, 'out_file', distancemap, "mask_file")
perivent_mask_init = pe.Node(fsl.maths.MathsCommand(),
name="perivent_mask_init")
perivent_mask_init.inputs.args = "-uthr 10 -bin"
wf.connect(distancemap, "distance_map", perivent_mask_init, "in_file")
perivent_mask = pe.Node(fsl.ApplyMask(), name="perivent_mask")
wf.connect(perivent_mask_init, "out_file", perivent_mask, "in_file")
wf.connect(inputnode, "tpl_t1w_brainmask", perivent_mask, "mask_file")
deepWM_mask_init = pe.Node(fsl.maths.MathsCommand(),
name="deepWM_mask_init")
deepWM_mask_init.inputs.args = "-thr 10 -bin"
wf.connect(distancemap, "distance_map", deepWM_mask_init, "in_file")
deepWM_mask = pe.Node(fsl.ApplyMask(), name="deepWM_mask")
wf.connect(deepWM_mask_init, "out_file", deepWM_mask, "in_file")
wf.connect(inputnode, "tpl_t1w_brainmask", deepWM_mask, "mask_file")
outputnode = pe.Node(niu.IdentityInterface(fields=[
"t1w_2_MNI_mat", "t1w_MNIspace", "t1w_2_MNI_warp",
"bianca_wm_mask_file", "vent_file", "distance_map", "perivent_mask",
"deepWM_mask"
]),
name='outputnode')
wf.connect(norm_wf, 'outputnode.t1w_2_MNI_mat', outputnode,
"t1w_2_MNI_mat")
wf.connect(norm_wf, 'outputnode.t1w_MNIspace', outputnode, "t1w_MNIspace")
wf.connect(norm_wf, 'outputnode.t1w_2_MNI_warp', outputnode,
"t1w_2_MNI_warp")
wf.connect(bianca_mask, 'mask_file', outputnode, "bianca_wm_mask_file")
wf.connect(bianca_mask, 'vent_file', outputnode, "vent_file")
wf.connect(distancemap, "distance_map", outputnode, "distance_map")
wf.connect(perivent_mask, "out_file", outputnode, "perivent_mask")
wf.connect(deepWM_mask, "out_file", outputnode, "deepWM_mask")
return wf