def dsi2metadata():
import nibabel.nicom.dicomreaders as dr
raw_dir = op.join(gconf.get_rawdata())
dsi_dir = op.join(raw_dir, 'DSI')
raw_glob = gconf.get_rawglob('diffusion')
diffme = gconf.get_diffusion_metadata()
try:
# extract bvals, bvects, affine from dsi and store them as .txt in NIFTI
data, affine, bval, bvect = dr.read_mosaic_dir(dsi_dir, raw_glob)
except Exception, e:
log.error("There was an exception: %s" % e)
return
from dipy.reconst.dti import Tensor
from dipy.reconst.dni import DiffusionNabla, EquatorialInversion
from dipy.reconst.dsi import DiffusionSpectrum, project_hemisph_bvecs
from dipy.tracking.propagation import EuDX
from dipy.align.aniso2iso import resample
from dipy.viz import fvtk
from visualize_dsi import show_blobs
#you need to switch to matthew's branch dicom-sorting for nibabel
from nibabel.nicom.dicomreaders import read_mosaic_dir
if __name__ == '__main__':
dirname='/home/eg309/Data/project01_dsi/connectome_0001/tp1/RAWDATA/DSI'
data,affine,bvals,bvecs = read_mosaic_dir(dirname,globber='mr*',sort_func='instance number')
bvecs[np.isnan(bvecs)]=0
#project identical b-vectors to the other hemisphere
bvecs2,pairs=project_hemisph_bvecs(bvals,bvecs)
#stop
#get voxel size
zooms=np.sqrt(np.sum(affine[:3,:3]**2,axis=0))
nzooms=(zooms[0],zooms[0],zooms[0])
#resample datasets
print(data.shape)
data,affine=resample(data,affine,zooms,nzooms)
print(data.shape)
#mask a bit the background or load the mask
