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):
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 static_build(self):
fssubjdir = self.fs
with local.tempdir() as tmpdir, BRAINSTools.env(
self.BRAINSTools_hash):
tmpoutdir = tmpdir / '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, '-o', dwi)
convertImage(self.dwimask, dwimask, self.BRAINSTools_hash)
convertImage(self.t2, t2, self.BRAINSTools_hash)
convertImage(self.t1, t1, self.BRAINSTools_hash)
convertImage(self.t2mask, t2mask, self.BRAINSTools_hash)
convertImage(self.t1mask, t1mask, self.BRAINSTools_hash)
script = local['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.BRAINSTools_hash)
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash):
slicecmd = unu["slice", "-a", "3", "-p", 0, "-i", self.dwi]
binarizecmd = unu["3op", "ifelse", "-", 1, 0]
gzipcmd = unu["save", "-e", "gzip", "-f", "nrrd", "-o",
self.output()]
(slicecmd | binarizecmd | gzipcmd) & FG
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash):
epi_py('--force',
'--dwi', self.dwi,
'--dwimask', self.dwimask,
'--t2', self.t2,
'--t2mask', self.t2mask,
'-o', self.output())
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash), ANTs.env(self.ANTs_hash):
epi_py('--force', '--typeCast',
'--dwi', self.dwi,
'--dwimask', self.dwimask,
'--t2', self.t2,
'--t2mask', self.t2mask,
'-o', self.output(),
'-n', NCPU)
def static_build(self):
fssubjdir = self.fs
with local.tempdir() as tmpdir, BRAINSTools.env(self.BRAINSTools_hash):
tmpoutdir = tmpdir / 'fsindwi'
tmpdwi = tmpdir / 'dwi.nrrd'
tmpdwimask = tmpdir / 'dwimask.nrrd'
dwiconvert_py('-i', self.dwi, '-o', tmpdwi)
convertImage(self.dwimask, tmpdwimask, self.BRAINSTools_hash)
fs2dwi_py['-f', fssubjdir, '-t', tmpdwi, '-m', tmpdwimask, '-o',
tmpoutdir, 'direct'] & FG
local.path(tmpoutdir / 'wmparcInDwi1mm.nii.gz').copy(self.output())
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 static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash), local.tempdir() as tmpdir:
moving = tmpdir / 'moving.nrrd'
movingmask = tmpdir / 'movingmask.nrrd'
fixed = tmpdir / 'fixed.nrrd'
out = tmpdir / 'fixedmask.nrrd'
convertImage(self.moving, moving, self.BRAINSTools_hash)
convertImage(self.moving_mask, movingmask, self.BRAINSTools_hash)
convertImage(self.fixed, fixed, self.BRAINSTools_hash)
makeRigidMask_py('-i', moving, '--labelmap', movingmask,
'--target', fixed, '-o', out)
out.move(self.output())
def static_build(self):
with local.tempdir() as tmpdir, BRAINSTools.env(self.BRAINSTools_hash), ANTs.env(self.ANTs_hash):
tmpdir = local.path(tmpdir)
tmpt1 = tmpdir / ('t1' + ''.join(self.t1.suffixes))
from plumbum.cmd import ConvertBetweenFileFormats
ConvertBetweenFileFormats[self.t1, tmpt1] & FG
trainingCsv = soft.trainingDataT1AHCC.get_path(
self.trainingDataT1AHCC_hash) / 'trainingDataT1AHCC-hdr.csv'
outPrefix= tmpdir / 'trainingDataT1'
atlas_py['csv', '--fusion', 'avg', '-t', tmpt1, '-o', tmpdir / 'trainingDataT1', '-n', NCPU,
trainingCsv] & FG
(tmpdir / 'trainingDataT1-mask.nrrd').copy(self.output())
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 static_build(self):
with local.tempdir() as tmpdir, BRAINSTools.env(self.BRAINSTools_hash):
tmpdir = local.path(tmpdir)
# antsRegistration can't handle a non-conventionally named file, so
# we need to pass in a conventionally named one
# TODO needed any more?
tmpt1 = tmpdir / ('t1' + ''.join(self.t1.suffixes))
from plumbum.cmd import ConvertBetweenFileFormats
ConvertBetweenFileFormats[self.t1, tmpt1] & FG
trainingCsv = soft.trainingDataT1AHCC.get_path(
self.trainingDataT1AHCC_hash) / 'trainingDataT1AHCC-hdr.csv'
atlas_py['csv', '--fusion', 'avg', '-t', tmpt1, '-o', tmpdir,
trainingCsv] & FG
(tmpdir / 'mask.nrrd').copy(self.output())
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash), local.tempdir() as tmpdir:
tmpdir = local.path(tmpdir)
tmpdwi = tmpdir / 'dwi.nrrd'
tmpdwimask = tmpdir / 'dwimask.nrrd'
dwiconvert_py('-i', self.dwi, '-o', tmpdwi)
convertImage(self.dwimask, tmpdwimask, self.BRAINSTools_hash)
params = ['--dwiFile', tmpdwi, '--maskFile', tmpdwimask,
'--seedsFile', tmpdwimask, '--recordTensors', '--tracts',
self.output()] + list(self.ukfparams)
ukfpath = soft.UKFTractography.get_path(self.UKFTractography_hash)
log.info(' Found UKF at {}'.format(ukfpath))
ukfbin = local[ukfpath]
# ukfbin(*params)
ukfbin.bound_command(*params) & 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 convertImage(i, o, bthash):
if i.suffixes == o.suffixes:
i.copy(o)
with BRAINSTools.env(bthash):
from plumbum.cmd import ConvertBetweenFileFormats
ConvertBetweenFileFormats(i, o)
def static_build(self):
soft.FreeSurfer.validate(self.FreeSurfer_version)
with BRAINSTools.env(self.BRAINSTools_hash), ANTs.env(self.ANTs_hash):
fs_py['-i', self.t1, '-m', self.t1mask, '-f', '-o', self.output()] & FG
def static_build(self):
self.output().delete()
with soft.tract_querier.env(self.tract_querier_hash), BRAINSTools.env(self.BRAINSTools_hash):
wmql_py['-i', self.ukf, '--fsindwi', self.fsindwi, '-o',
self.output(), '-n', NCPU] & 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
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash), \
local.tempdir() as tmpdir:
nrrd = tmpdir / 'strct.nrrd'
convertImage(self.strct, nrrd, self.BRAINSTools_hash)
alignAndCenter_py['-i', nrrd, '-o', self.output()] & FG
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 static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash), \
local.tempdir() as tmpdir:
bet_py('--force', '-f', self.bet_threshold, '-i', self.dwi, '-o',
self.output())
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash):
eddy_py['-i', self.dwi, '-o', self.output(), '--force'] & LOG
def static_build(self):
with BRAINSTools.env(self.BRAINSTools_hash), local.tempdir() as tmpdir:
inputnrrd = tmpdir / 'inputdwi.nrrd'
dwiconvert_py['-f', '-i', self.dwi, '-o', inputnrrd] & LOG
alignAndCenter_py['-i', inputnrrd, '-o', self.output()] & LOG
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:
nrrd = tmpdir / 'strct.nrrd'
convertImage(self.strct.output(), nrrd, self.bthash)
alignAndCenter_py['-i', nrrd, '-o', self.output()] & FG