def hcp_workflow(name='Evaluation_HCP', settings={},
map_metric=False, compute_fmb=False):
"""
The pyacwereg evaluation workflow for the human connectome project (HCP)
"""
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu
from nipype.interfaces import io as nio
from nipype.algorithms.mesh import ComputeMeshWarp, WarpPoints
from nipype.algorithms.misc import AddCSVRow
from nipype.workflows.dmri.fsl.artifacts import sdc_fmb
from pyacwereg import data
from pyacwereg.interfaces.utility import (ExportSlices, TileSlicesGrid,
SlicesGridplot)
from pyacwereg.workflows.registration import regseg_wf, sdc_t2b
from pyacwereg.workflows import evaluation as ev
from pyacwereg.workflows.preprocess import preprocess
from pyacwereg.workflows.fieldmap import process_vsm
from pyacwereg.workflows.dti import mrtrix_dti
wf = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['subject_id', 'data_dir']), name='inputnode')
inputnode.inputs.data_dir = settings['data_dir']
inputnode.iterables = [('subject_id', settings['subject_id'])]
# Generate the distorted set, including surfaces
pre = preprocess()
rdti = mrtrix_dti('ReferenceDTI')
wdti = mrtrix_dti('WarpedDTI')
mdti = pe.Node(niu.Merge(2), name='MergeDTI')
wf.connect([
(inputnode, pre, [('subject_id', 'inputnode.subject_id'),
('data_dir', 'inputnode.data_dir')]),
(pre, rdti, [('outputnode.dwi', 'inputnode.in_dwi'),
('outputnode.dwi_mask', 'inputnode.in_mask'),
('outputnode.bvec', 'inputnode.in_bvec'),
('outputnode.bval', 'inputnode.in_bval')]),
(pre, wdti, [('outputnode.warped_dwi', 'inputnode.in_dwi'),
('outputnode.warped_msk', 'inputnode.in_mask'),
('outputnode.bvec', 'inputnode.in_bvec'),
('outputnode.bval', 'inputnode.in_bval')]),
(wdti, mdti, [('outputnode.fa', 'in1'),
('outputnode.md', 'in2')]),
])
regseg = regseg_wf(usemask=True)
regseg.inputs.inputnode.options = data.get('regseg_hcp')
exprs = pe.Node(ExportSlices(slices=[38, 48, 57, 67, 76, 86],
axis=['axial', 'sagittal']), name='ExportREGSEG')
gridrs = pe.Node(SlicesGridplot(
label=['regseg', 'regseg'], slices=[38, 48, 57, 67, 76, 86],
view=['axial', 'sagittal']), name='GridPlotREGSEG')
meshrs = pe.MapNode(ComputeMeshWarp(),
iterfield=['surface1', 'surface2'],
name='REGSEGSurfDistance')
csvrs = pe.Node(AddCSVRow(in_file=settings['out_csv']),
name="REGSEGAddRow")
csvrs.inputs.method = 'REGSEG'
wf.connect([
(mdti, regseg, [('out', 'inputnode.in_fixed')]),
(pre, regseg, [('outputnode.surf', 'inputnode.in_surf'),
('outputnode.warped_msk', 'inputnode.in_mask')]),
(pre, exprs, [('outputnode.warped_surf', 'sgreen')]),
(regseg, exprs, [('outputnode.out_surf', 'syellow')]),
(wdti, exprs, [('outputnode.fa', 'reference')]),
(exprs, gridrs, [('out_files', 'in_files')]),
(pre, meshrs, [('outputnode.warped_surf', 'surface1')]),
(regseg, meshrs, [('outputnode.out_surf', 'surface2')]),
(inputnode, csvrs, [('subject_id', 'subject_id')]),
(meshrs, csvrs, [('distance', 'surf_dist')])
])
if compute_fmb:
cmethod0 = sdc_fmb()
selbmap = pe.Node(niu.Split(splits=[1, 1], squeeze=True),
name='SelectBmap')
dfm = process_vsm()
dfm.inputs.inputnode.scaling = 1.0
dfm.inputs.inputnode.enc_dir = 'y-'
wrpsurf = pe.MapNode(WarpPoints(), iterfield=['points'],
name='UnwarpSurfs')
export0 = pe.Node(ExportSlices(slices=[38, 48, 57, 67, 76, 86],
axis=['axial', 'sagittal']), name='ExportFMB')
mesh0 = pe.MapNode(ComputeMeshWarp(),
iterfield=['surface1', 'surface2'],
name='FMBSurfDistance')
grid0 = pe.Node(SlicesGridplot(
label=['FMB']*2, slices=[38, 48, 57, 67, 76, 86],
view=['axial', 'sagittal']), name='GridPlotFMB')
csv0 = pe.Node(AddCSVRow(in_file=settings['out_csv']),
name="FMBAddRow")
csv0.inputs.method = 'FMB'
wf.connect([
(pre, cmethod0, [
('outputnode.warped_dwi', 'inputnode.in_file'),
('outputnode.warped_msk', 'inputnode.in_mask'),
('outputnode.bval', 'inputnode.in_bval'),
('outputnode.mr_param', 'inputnode.settings')]),
(pre, selbmap, [('outputnode.bmap_wrapped', 'inlist')]),
(selbmap, cmethod0, [('out1', 'inputnode.bmap_mag'),
('out2', 'inputnode.bmap_pha')]),
(cmethod0, dfm, [('outputnode.out_vsm', 'inputnode.vsm')]),
(pre, dfm, [
('outputnode.warped_msk', 'inputnode.reference')]),
(dfm, wrpsurf, [('outputnode.dfm', 'warp')]),
(pre, wrpsurf, [('outputnode.surf', 'points')])
(wrpsurf, export0, [('out_points', 'syellow')]),
(pre, export0, [('outputnode.warped_surf', 'sgreen')]),
(wdti, export0, [('outputnode.fa', 'reference')]),
(export0, grid0, [('out_files', 'in_files')]),
(pre, mesh0, [('outputnode.warped_surf', 'surface1')]),
(wrpsurf, mesh0, [('out_points', 'surface2')]),
(inputnode, csv0, [('subject_id', 'subject_id')]),
(mesh0, csv0, [('distance', 'surf_dist')])
])
cmethod1 = sdc_t2b(num_threads=settings['nthreads'])
export1 = pe.Node(ExportSlices(slices=[38, 48, 57, 67, 76, 86],
axis=['axial', 'sagittal']), name='ExportT2B')
grid1 = pe.Node(SlicesGridplot(
label=['T2B']*2, slices=[38, 48, 57, 67, 76, 86],
view=['axial', 'sagittal']), name='GridPlotT2B')
mesh1 = pe.MapNode(ComputeMeshWarp(),
iterfield=['surface1', 'surface2'],
name='T2BSurfDistance')
csv1 = pe.Node(AddCSVRow(in_file=settings['out_csv']),
name="T2BAddRow")
csv1.inputs.method = 'T2B'
wf.connect([
(pre, cmethod1, [
('outputnode.warped_dwi', 'inputnode.in_dwi'),
('outputnode.warped_msk', 'inputnode.dwi_mask'),
('outputnode.t2w_brain', 'inputnode.in_t2w'),
('outputnode.t1w_mask', 'inputnode.t2w_mask'),
('outputnode.surf', 'inputnode.in_surf'),
('outputnode.bval', 'inputnode.in_bval'),
('outputnode.mr_param', 'inputnode.in_param')]),
(cmethod1, export1, [('outputnode.out_surf', 'syellow')]),
(pre, export1, [('outputnode.warped_surf', 'sgreen')]),
(wdti, export1, [('outputnode.fa', 'reference')]),
(export1, grid1, [('out_files', 'in_files')]),
(pre, mesh1, [('outputnode.warped_surf', 'surface1')]),
(cmethod1, mesh1, [('outputnode.out_surf', 'surface2')]),
(inputnode, csv1, [('subject_id', 'subject_id')]),
(mesh1, csv1, [('distance', 'surf_dist')])
])
tile = pe.Node(TileSlicesGrid(), name='TileGridplots')
csvtile = pe.Node(AddCSVRow(
in_file=op.join(op.dirname(settings['out_csv']), 'tiles.csv')),
name="TileAddRow")
wf.connect([
(inputnode, tile, [('subject_id', 'out_file')]),
(gridrs, tile, [('out_file', 'in_reference')]),
(grid1, tile, [('out_file', 'in_competing')]),
(tile, csvtile, [('out_file', 'names')])
])
if map_metric:
out_csv = op.abspath(op.join(name, 'energiesmapping.csv'))
mapen = ev.map_energy(out_csv=out_csv)
wf.connect([
(inputnode, mapen, [('subject_id', 'inputnode.subject_id')]),
(regseg, mapen, [('outputnode.out_enh', 'inputnode.reference'),
('outputnode.reg_msk', 'inputnode.in_mask')]),
(pre, mapen, [
('outputnode.warped_surf', 'inputnode.surfaces0'),
('outputnode.surf', 'inputnode.surfaces1')])
])
return wf
def all_surfaces(name='Surfaces', gen_outer=False):
import nipype.pipeline.engine as pe
from nipype.interfaces.io import JSONFileGrabber
import pyacwereg.data as data
inputnode = pe.Node(niu.IdentityInterface(
fields=['aseg', 'norm', 'in_mask']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_surf']), name='outputnode')
readls = pe.Node(JSONFileGrabber(in_file=data.get('model_labels')),
name='ReadModelLabels')
nsurfs = 0
tha = extract_surface(name='ThalSurface')
tha.inputs.inputnode.name = '%02d.thalamus' % nsurfs
nsurfs += 1
csf = extract_surface(name='VdGMSurface')
csf.inputs.inputnode.name = '%02d.csf_dgm' % nsurfs
nsurfs += 1
bstem = extract_surface(name='stemSurface')
bstem.inputs.inputnode.name = '%02d.bstem' % nsurfs
nsurfs += 1
wm = extract_surface(name='WMSurface')
wm.inputs.inputnode.name = '%02d.white' % nsurfs
nsurfs += 1
cgm = extract_surface(name='cbGMSurface')
cgm.inputs.inputnode.name = '%02d.cgm' % nsurfs
nsurfs += 1
pial = extract_surface(name='PialSurface')
pial.inputs.inputnode.name = '%02d.pial' % nsurfs
nsurfs += 1
if gen_outer:
nsurfs = nsurfs + 1
m = pe.Node(niu.Merge(nsurfs), name='MergeSurfs')
wf = pe.Workflow(name=name)
wf.connect([
(inputnode, tha, [('aseg', 'inputnode.aseg'),
('norm', 'inputnode.norm')]),
(readls, tha, [('thal_labels', 'inputnode.labels')]),
(tha, m, [('outputnode.out_surf', 'in1')]),
(inputnode, csf, [('aseg', 'inputnode.aseg'),
('norm', 'inputnode.norm')]),
(readls, csf, [('csf_dgm_labels', 'inputnode.labels')]),
(csf, m, [('outputnode.out_surf', 'in2')]),
(inputnode, bstem, [('aseg', 'inputnode.aseg'),
('norm', 'inputnode.norm')]),
(readls, bstem, [('bstem_labels', 'inputnode.labels')]),
(bstem, m, [('outputnode.out_surf', 'in3')]),
(inputnode, wm, [('aseg', 'inputnode.aseg'),
('norm', 'inputnode.norm')]),
(readls, wm, [('wm_labels', 'inputnode.labels')]),
(wm, m, [('outputnode.out_surf', 'in4')]),
(inputnode, cgm, [('aseg', 'inputnode.aseg'),
('norm', 'inputnode.norm')]),
(readls, cgm, [('cgm_labels', 'inputnode.labels')]),
(cgm, m, [('outputnode.out_surf', 'in5')]),
(inputnode, pial, [('aseg', 'inputnode.aseg'),
('norm', 'inputnode.norm')]),
(readls, pial, [('gm_labels', 'inputnode.labels')]),
(pial, m, [('outputnode.out_surf', 'in6')]),
(m, outputnode, [('out', 'out_surf')])
])
if gen_outer:
msk = extract_surface(name='MaskSurf')
msk.inputs.inputnode.labels = [1]
msk.inputs.inputnode.name = '%01d.outer' % nsurfs - 1
wf.connect([
(inputnode, msk, [('in_mask', 'inputnode.aseg'),
('in_mask', 'inputnode.norm')]),
(msk, m, [('outputnode.out_surf', 'in%d' % nsurfs)])
])
return wf
