def build(self):
needDeps(self)
fssubjdir = self.fs.output().dirname.dirname
with TemporaryDirectory() as tmpdir, BRAINSTools.env(self.bthash):
tmpoutdir = tmpdir / (self.caseid + '-fsindwi')
dwi = tmpdir / 'dwi.nrrd'
dwimask = tmpdir / 'dwimask.nrrd'
fs = tmpdir / 'fs'
t2 = tmpdir / 't2.nrrd'
t1 = tmpdir / 't1.nrrd'
t1mask = tmpdir / 't1mask.nrrd'
t2mask = tmpdir / 't2mask.nrrd'
fssubjdir.copy(fs)
dwiconvert_py('-i', self.dwi.output(), '-o', dwi)
convertImage(self.dwimask.output(), dwimask, self.bthash)
convertImage(self.t2.output(), t2, self.bthash)
convertImage(self.t1.output(), t1, self.bthash)
convertImage(self.t2mask.output(), t2mask, self.bthash)
convertImage(self.t1mask.output(), t1mask, self.bthash)
script = local['pnlpipe_pipelines/pnlscripts/old/fs2dwi_T2.sh']
script['--fsdir', fs, '--dwi', dwi, '--dwimask', dwimask, '--t2',
t2, '--t2mask', t2mask, '--t1', t1, '--t1mask', t1mask,
'-o', tmpoutdir] & FG
convertImage(tmpoutdir / 'wmparc-in-bse.nrrd', self.output(),
self.bthash)
def build(self):
needDeps(self)
with BRAINSTools.env(self.bthash):
from pnlscripts.util.scripts import epi_py
epi_py('--force', '--dwi', self.dwi.output(), '--dwimask',
self.dwimask.output(), '--t2', self.t2.output(), '--t2mask',
self.t2mask.output(), '-o', self.output())
def build(self, db):
needDeps(self, self.deps, db)
with HCPPipelines.env(
self.version_HCPPipelines), TemporaryDirectory() as tmpdir:
preproc = local[HCPPipelines.get_path(self.version_HCPPipelines) /
'DiffusionPreprocessing/DiffPreprocPipeline.sh']
posPaths = [n.output() for n in self.posDwis]
negPaths = [n.output() for n in self.negDwis]
datadir = tmpdir / 'hcp/data'
from os import getpid
hcpdir = OUTDIR / self.caseid / 'hcp-{}'.format(getpid())
datadir = hcpdir / 'data'
try:
preproc['--path={}'.format(OUTDIR),
'--subject={}'.format(self.caseid),
'--PEdir={}'.format(self.peDir), '--posData=' +
'@'.join(posPaths), '--negData=' + '@'.join(negPaths),
'--echospacing={}'.format(self.echoSpacing),
'--gdcoeffs=NONE',
'--dwiname=hcp-{}'.format(getpid())] & FG
except ProcessExecutionError as e:
if not (datadir / 'data.nii.gz').exists():
print(e)
log.error("HCP failed to make '{}'".format(datadir /
'data.nii.gz'))
(OUTDIR / self.caseid / 'T1w').delete()
sys.exit(1)
(OUTDIR / self.caseid / 'T1w').delete()
(datadir / 'data.nii.gz').move(self.output())
(datadir / 'bvals').move(self.output().with_suffix('.bval',
depth=2))
(datadir / 'bvecs').move(self.output().with_suffix('.bvec',
depth=2))
def build(self, db):
needDeps(self, self.deps, db)
measureTracts_py = local[
'pnlpipe_pipelines/pnlscripts/measuretracts/measureTracts.py']
vtks = self.wmql.output().up() // '*.vtk'
measureTracts_py['-f', '-c', 'caseid', 'algo', '-v', self.caseid,
self.wmql.showCompressedDAG(), '-o',
self.output(), '-i', vtks] & FG
def build(self, db):
needDeps(self, self.deps, db)
# make sure FREESURFER_HOME is set to right version
pnlpipe_software.FreeSurfer.validate(self.version_FreeSurfer)
from pnlscripts.util.scripts import fs_py
fs_py['-i',
self.t1.output(), '-m',
self.t1mask.output(), '-f', '-o',
self.output().dirname.dirname] & FG
def build(self, db):
needDeps(self, self.deps, db)
if self.output().up().exists():
self.output().up().delete()
with tract_querier.env(self.tqhash):
from pnlscripts.util.scripts import wmql_py
wmql_py['-i',
self.ukf.output(), '--fsindwi',
self.fsindwi.output(), '-o',
self.output().dirname] & FG
def build(self, db):
needDeps(self, self.deps, db)
fssubjdir = self.fs.output().dirname.dirname
with TemporaryDirectory() as tmpdir, BRAINSTools.env(self.bthash):
tmpoutdir = tmpdir / (self.caseid + '-fsindwi')
tmpdwi = tmpdir / 'dwi.nrrd'
tmpdwimask = tmpdir / 'dwimask.nrrd'
dwiconvert_py('-i', self.dwi.output(), '-o', tmpdwi)
convertImage(self.dwimask.output(), tmpdwimask, self.bthash)
fs2dwi_py['-f', fssubjdir, '-t', tmpdwi, '-m', tmpdwimask, '-o',
tmpoutdir, 'direct'] & FG
local.path(tmpoutdir / 'wmparcInDwi1mm.nii.gz').copy(self.output())
def build(self):
from plumbum.cmd import ImageMath
needDeps(self)
with TemporaryDirectory() as tmpdir, pnlpipe_software.BRAINSTools.env(
self.hash_BRAINSTools):
tmptxt = tmpdir / 'dice.txt'
ImageMath[3, tmptxt, "DiceAndMinDistSum",
self.maskManual.path(),
self.mask.path()] & FG
with open(tmptxt, 'r') as f:
coeff = f.read().split(' ')[-1]
with open(self.output(), 'w') as f:
f.write(coeff)
def build(self, db):
needDeps(self, self.deps, db)
with TemporaryDirectory() as tmpdir, BRAINSTools.env(self.bthash):
tmpdir = local.path(tmpdir)
# antsRegistration can't handle a non-conventionally named file, so
# we need to pass in a conventionally named one
tmpt1 = tmpdir / ('t1' + ''.join(self.t1.output().suffixes))
from plumbum.cmd import ConvertBetweenFileFormats
ConvertBetweenFileFormats[self.t1.output(), tmpt1] & FG
trainingCsv = trainingDataT1AHCC.get_path(
self.trainingDataT1AHCC) / 'trainingDataT1AHCC-hdr.csv'
atlas_py['csv', '--fusion', 'avg', '-t', tmpt1, '-o', tmpdir,
trainingCsv] & FG
(tmpdir / 'mask.nrrd').copy(self.output())
def build(self):
needDeps(self)
with TemporaryDirectory() as tmpdir, local.cwd(
tmpdir), pnlpipe_software.mrtrix3.env(self.hash_mrtrix3):
from plumbum.cmd import maskfilter
slicerDir = pnlpipe_software.Slicer.get_path(
self.version_Slicer).dirname
Slicer = local[slicerDir / 'Slicer']
Slicer['--launch', slicerDir / 'DiffusionWeightedVolumeMasking',
self.dwi.path(), 'b0.nrrd', 'otsumask.nrrd',
'--baselineBValueThreshold', '1000', '--removeislands'] & FG
Slicer['--launch', 'ResampleScalarVolume', 'otsumask.nrrd',
'otsumask.nii'] & FG
maskfilter['-scale', 2, 'otsumask.nii', 'clean',
self.output(), '-force'] & FG
def build(self, db):
needDeps(self, self.deps, db)
with BRAINSTools.env(self.bthash), TemporaryDirectory() as tmpdir:
from pnlscripts.util.scripts import makeRigidMask_py
moving = tmpdir / 'moving.nrrd'
movingmask = tmpdir / 'movingmask.nrrd'
fixed = tmpdir / 'fixed.nrrd'
out = tmpdir / 'fixedmask.nrrd'
convertImage(self.movingStrct.output(), moving, self.bthash)
convertImage(self.movingStrctMask.output(), movingmask,
self.bthash)
convertImage(self.fixedStrct.output(), fixed, self.bthash)
makeRigidMask_py('-i', moving, '--labelmap', movingmask,
'--target', fixed, '-o', out)
out.move(self.output())
def build(self):
needDeps(self)
with BRAINSTools.env(self.bthash), TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
tmpdwi = tmpdir / 'dwi.nrrd'
tmpdwimask = tmpdir / 'dwimask.nrrd'
dwiconvert_py('-i', self.dwi.output(), '-o', tmpdwi)
convertImage(self.dwimask.output(), tmpdwimask, self.bthash)
params = [
'--dwiFile', tmpdwi, '--maskFile', tmpdwimask, '--seedsFile',
tmpdwimask, '--recordTensors', '--tracts',
self.output()
] + defaultUkfParams
ukfpath = UKFTractography.get_path(self.ukfhash)
log.info(' Found UKF at {}'.format(ukfpath))
ukfbin = local[ukfpath]
ukfbin(*params)
def build(self, db):
needDeps(self, self.deps, db)
with BRAINSTools.env(self.bthash), TemporaryDirectory() as tmpdir:
nrrd = tmpdir / 'strct.nrrd'
convertImage(self.strct.output(), nrrd, self.bthash)
alignAndCenter_py['-i', nrrd, '-o', self.output()] & FG
def build(self):
needDeps(self)
with BRAINSTools.env(self.bthash), TemporaryDirectory() as tmpdir:
bet_py('--force', '-f', self.threshold, '-i', self.dwi.output(),
'-o', self.output())
def build(self, db):
needDeps(self, self.deps, db)
with BRAINSTools.env(self.bthash), TemporaryDirectory() as tmpdir:
tmpdwi = tmpdir / (self.caseid + '-dwi.nrrd')
dwiconvert_py['-f', '-i', self.dwi.output(), '-o', tmpdwi] & FG
alignAndCenter_py['-i', tmpdwi, '-o', self.output()] & FG
def build(self, db):
needDeps(self, self.deps, db)
with BRAINSTools.env(self.bthash):
eddy_py['-i',
self.dwi.output(), '-o',
self.output(), '--force'] & FG
