"""Contains functions for making a whitematter mask
"""
import shutil
import tempfile
import subprocess as sp
import numpy as np
#from . import utils
from .database import db
from .options import config
from .xfm import Transform
fsl_prefix = config.get('basic', 'fsl_prefix')
[docs]
def brainmask(outfile, subject):
raw = db.get_anat(subject, type='raw').get_filename()
print('Brain masking anatomical...')
cmd = '{fsl_prefix}bet {raw} {bet} -B -v'.format(fsl_prefix=fsl_prefix, raw=raw, bet=outfile)
print("Calling: %s"%cmd)
assert sp.call(cmd, shell=True) == 0, "Error calling fsl-bet"
[docs]
def whitematter(outfile, subject, do_voxelize=False):
try:
if not do_voxelize:
raise IOError
else:
voxelize(outfile, subject, surf="wm")
except IOError:
import nibabel
try:
cache = tempfile.mkdtemp()
print ("Attempting to segment the brain with freesurfer...")
bet2 = db.get_anat(subject, type='raw_wm').get_filename()
vol = nibabel.load('{bet2}'.format(bet2=bet2))
vol_data = vol.get_fdata()
print(vol_data.shape)
new_data = vol_data.copy()
new_data[new_data==250] = 0
new_data[new_data>0] = 1
wm_freesurf = nibabel.Nifti1Image(new_data, vol.affine, header=vol.header)
wm_freesurf.to_filename(outfile)
except:
cache = tempfile.mkdtemp()
print("Attempt with freesurfer failed, trying again with FSL...")
bet = db.get_anat(subject, type='brainmask').get_filename()
cmd = '{fsl_prefix}fast -o {cache}/fast {bet}'.format(fsl_prefix=fsl_prefix, cache=cache, bet=bet)
assert sp.call(cmd, shell=True) == 0, "Error calling fsl-fast"
wmfl = 'fast_pve_2'
arr = np.asarray(nibabel.load('{cache}/{wmseg}.nii.gz'.format(cache=cache,wmseg=wmfl)).get_fdata())
if arr.sum() == 0:
from warnings import warn
warn('"fsl-fast" with default settings failed. Trying no pve, no bias correction...')
cmd = '{fsl_prefix}fast -g --nopve --nobias -o {cache}/fast {bet}'.format(fsl_prefix=fsl_prefix, cache=cache, bet=bet)
assert sp.call(cmd, shell=True) == 0, "Error calling fsl-fast"
wmfl = 'fast_seg_2'
cmd = '{fsl_prefix}fslmaths {cache}/{wmfl} -thr 0.5 -bin {out}'.format(fsl_prefix=fsl_prefix, cache=cache, wmfl=wmfl, out=outfile)
assert sp.call(cmd, shell=True) == 0, 'Error calling fsl-maths'
# check generated mask succeeded
arr = np.asarray(nibabel.load('{outfl}'.format(outfl=outfile)).get_fdata())
assert arr.sum() >= 0, 'Error with generated whitematter mask.'
finally:
shutil.rmtree(cache)
[docs]
def voxelize(outfile, subject, surf='wm', mp=True):
'''Voxelize the whitematter surface to generate the white matter mask'''
import nibabel
from . import polyutils
nib = db.get_anat(subject, "raw")
shape = nib.get_shape()
vox = np.zeros(shape, dtype=bool)
for pts, polys in db.get_surf(subject, surf, nudge=False):
xfm = Transform(np.linalg.inv(nib.affine), nib)
vox += polyutils.voxelize(xfm(pts), polys, shape=shape, center=(0,0,0), mp=mp).astype('bool')
nib = nibabel.Nifti1Image(vox, nib.affine, header=nib.header)
nib.to_filename(outfile)
return vox.T