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):
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 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