Registration of the FA image to the T1 image
--------------------------------------------
Register the FA image to the T1 image and generate a 'cortex_whitematter-mask'
and 'cortex_gyri-labels' in the FA space. It also generate seed regions
to compute the connectivity matrix in the FA space in the 'gyri' folder.
"""
cortex_outdir = os.path.join(outdir, "cortex")
if not os.path.isdir(cortex_outdir):
os.mkdir(cortex_outdir)
if len(os.listdir(cortex_outdir)) == 0:
mask_file, label_file, seeds, reg_file, trf_file = cortex(
t1_file,
fsdir,
cortex_outdir,
dest_file=fa_file,
generate_mask=True,
generate_seeds=True)
else:
seeds_outdir = os.path.join(cortex_outdir, "gyri")
reg_file = os.path.join(cortex_outdir, "cortex_dest_to_t1.nii.gz")
mask_file = os.path.join(cortex_outdir, "cortex_mask.nii.gz")
label_file = os.path.join(cortex_outdir, "cortex_gyri_labels.nii.gz")
for restored_file in [reg_file, mask_file]:
if not os.path.isfile(restored_file):
raise IOError("FileDoesNotExist: '{0}'.".format(restored_file))
if not os.path.isdir(seeds_outdir):
raise IOError("DirectoryDoesNotExist: '{0}'.".format(seeds_outdir))
seeds = [os.path.join(seeds_outdir, name) for
name in os.listdir(seeds_outdir)]
"""
Registration of the FA image to the T1 image
--------------------------------------------
Register the FA image to the T1 image and generate a 'cortex_whitematter-mask'
and 'cortex_gyri-labels' in the FA space. It also generate seed regions
to compute the connectivity matrix in the FA space in the 'gyri' folder.
"""
cortex_outdir = os.path.join(outdir, "cortex")
if not os.path.isdir(cortex_outdir):
os.mkdir(cortex_outdir)
if len(os.listdir(cortex_outdir)) == 0:
mask_file, _, _, reg_file, trf_file = cortex(t1_file,
fsdir,
cortex_outdir,
dest_file=fa_file,
generate_mask=True,
generate_seeds=False)
if use_t1_space:
_, label_file, _, _, _ = cortex(t1_file,
fsdir,
cortex_outdir,
generate_mask=False,
generate_seeds=False)
else:
reg_file = os.path.join(cortex_outdir, "cortex_dest_to_t1.nii.gz")
trf_file = os.path.join(cortex_outdir, "cortex_dest_to_t1.trf")
mask_file = os.path.join(cortex_outdir, "cortex_mask.nii.gz")
label_file = os.path.join(cortex_outdir, "cortex_gyri_labels.nii.gz")
for restored_file in [reg_file, trf_file, mask_file, label_file]:
Registration of the FA image to the T1 image
--------------------------------------------
Register the FA image to the T1 image and generate a 'cortex_whitematter-mask'
and 'cortex_gyri-labels' in the FA space. It also generate seed regions
to compute the connectivity matrix in the FA space in the 'gyri' folder.
"""
cortex_outdir = os.path.join(outdir, "cortex")
if not os.path.isdir(cortex_outdir):
os.mkdir(cortex_outdir)
if len(os.listdir(cortex_outdir)) == 0:
mask_file, _, _, reg_file, trf_file = cortex(
t1_file,
fsdir,
cortex_outdir,
dest_file=fa_file,
generate_mask=True,
generate_seeds=False)
if use_t1_space:
_, label_file, _, _, _ = cortex(
t1_file,
fsdir,
cortex_outdir,
generate_mask=False,
generate_seeds=False)
else:
reg_file = os.path.join(cortex_outdir, "cortex_dest_to_t1.nii.gz")
trf_file = os.path.join(cortex_outdir, "cortex_dest_to_t1.trf")
mask_file = os.path.join(cortex_outdir, "cortex_mask.nii.gz")
