def add_raw2connectome(connectome, type):
log.info("Adding raw data to connectome (%s)..." % type)
nifti_dir = op.join(gconf.get_nifti())
cvol = None
if type == 'rawdiffusion':
if gconf.diffusion_imaging_model == 'DSI':
if op.exists(op.join(nifti_dir, 'DSI.nii.gz')):
cvol = cf.CVolume(name="Raw Diffusion",
src=op.join(nifti_dir, 'DSI.nii.gz'),
fileformat='Nifti1GZ',
dtype='DSI')
elif gconf.diffusion_imaging_model == 'DTI':
if op.exists(op.join(nifti_dir, 'DTI.nii.gz')):
cvol = cf.CVolume(name="Raw Diffusion",
src=op.join(nifti_dir, 'DTI.nii.gz'),
fileformat='Nifti1GZ',
dtype='DTI')
elif gconf.diffusion_imaging_model == 'QBALL':
if op.exists(op.join(nifti_dir, 'QBALL.nii.gz')):
cvol = cf.CVolume(name="Raw Diffusion",
src=op.join(nifti_dir, 'QBALL.nii.gz'),
fileformat='Nifti1GZ',
dtype='QBALL')
elif type == 'rawT1':
if op.exists(op.join(nifti_dir, 'T1.nii.gz')):
cvol = cf.CVolume(name="Raw T1 image",
src=op.join(nifti_dir, 'T1.nii.gz'),
fileformat='Nifti1GZ',
dtype='T1-weighted')
elif type == 'rawT2':
if op.exists(op.join(nifti_dir, 'T2.nii.gz')):
cvol = cf.CVolume(name="Raw T2 image",
src=op.join(nifti_dir, 'T2.nii.gz'),
fileformat='Nifti1GZ',
dtype='T2-weighted')
if not cvol is None:
connectome.add_connectome_volume(cvol)
def add_scalars2connectome(connectome, type):
log.info("Adding scalar fields to connectome...")
scalarpath = gconf.get_cmp_scalars()
import gzip
if type == 'gfa':
if gconf.diffusion_imaging_model == 'DSI':
if op.exists(op.join(scalarpath, 'dsi_gfa.nii.gz')):
cvol = cf.CVolume(name="GFA Scalar Map",
src=op.join(scalarpath, 'dsi_gfa.nii.gz'),
fileformat='Nifti1GZ',
dtype='GFA')
connectome.add_connectome_volume(cvol)
elif type == 'skewness':
if gconf.diffusion_imaging_model == 'DSI':
if op.exists(op.join(scalarpath, 'dsi_skewness.nii.gz')):
cvol = cf.CVolume(name="Skewness Scalar Map",
src=op.join(scalarpath, 'dsi_skewness.nii.gz'),
fileformat='Nifti1GZ',
dtype='GFA')
connectome.add_connectome_volume(cvol)
elif type == 'kurtosis':
if gconf.diffusion_imaging_model == 'DSI':
if op.exists(op.join(scalarpath, 'dsi_kurtosis.nii.gz')):
cvol = cf.CVolume(name="Kurtosis Scalar Map",
src=op.join(scalarpath, 'dsi_kurtosis.nii.gz'),
fileformat='Nifti1GZ',
dtype='GFA')
connectome.add_connectome_volume(cvol)
elif type == 'P0':
if gconf.diffusion_imaging_model == 'DSI':
if op.exists(op.join(scalarpath, 'dsi_P0.nii.gz')):
cvol = cf.CVolume(name="P0 Scalar Map",
src=op.join(scalarpath, 'dsi_P0.nii.gz'),
fileformat='Nifti1GZ',
dtype='P0')
connectome.add_connectome_volume(cvol)
def add_roiseg2connectome(connectome):
log.info("Adding ROI segmentation to connectome...")
# add about everything
reg_path = gconf.get_cmp_tracto_mask()
asegf = op.join(reg_path, 'aseg.nii.gz')
ribbonf = op.join(reg_path, 'ribbon.nii.gz')
fsmaskf = op.join(reg_path, 'fsmask_1mm.nii.gz')
unkf = op.join(reg_path, 'cc_unknown.nii.gz')
if op.exists(asegf):
cvol = cf.CVolume(name="Aseg segmentation volume",
src=asegf,
fileformat='Nifti1GZ',
dtype='Segmentation')
connectome.add_connectome_volume(cvol)
if op.exists(ribbonf):
cvol = cf.CVolume(name="Ribbon segmentation volume",
src=ribbonf,
fileformat='Nifti1GZ',
dtype='Segmentation')
connectome.add_connectome_volume(cvol)
if op.exists(fsmaskf):
cvol = cf.CVolume(name="White matter mask",
src=fsmaskf,
fileformat='Nifti1GZ',
dtype='Segmentation')
connectome.add_connectome_volume(cvol)
if op.exists(unkf):
cvol = cf.CVolume(name="CC and Unknown",
src=unkf,
fileformat='Nifti1GZ',
dtype='Segmentation')
connectome.add_connectome_volume(cvol)
# is original T1 space
for p in gconf.parcellation.keys():
log.info("Adding volume ROI for resolution (original space): %s" % p)
file = op.join(op.join(reg_path, p), 'ROI_HR_th.nii.gz')
if op.exists(file):
cvol = cf.CVolume(name="ROI Volume %s" % p,
src=file,
fileformat='Nifti1GZ',
dtype='Segmentation')
connectome.add_connectome_volume(cvol)
# in space registred to b0
reg_path = gconf.get_cmp_tracto_mask_tob0()
for p in gconf.parcellation.keys():
log.info("Adding volume ROI for resolution (in b0 space): %s" % p)
file = op.join(op.join(reg_path, p), 'ROI_HR_th.nii.gz')
if op.exists(file):
cvol = cf.CVolume(name="ROI Scale %s (b0 space)" % p,
src=file,
fileformat='Nifti1GZ',
dtype='Segmentation')
connectome.add_connectome_volume(cvol)