def get_roi(atlas, name):
""" Get the an roi (a nifti1 object) by <name> from <atlas>. """
# Set the path for the named roi
# and try to open it.
path = os.path.join(roi.__path__[0], 'atlases', atlas, 'rois', name)
try:
nifti = read_nifti(path)
# If name can't be loaded you may need to run
# create_rois, tell the user that.
except IOError, err:
print("Could not load <name>. Try create_rois() or open_atlases()")
raise IOError(err)
def get_roi(atlas, name):
""" Get the an roi (a nifti1 object) by <name> from <atlas>. """
# Set the path for the named roi
# and try to open it.
path = os.path.join(roi.__path__[0], 'atlases', atlas, 'rois', name)
try:
nifti = read_nifti(path)
# If name can't be loaded you may need to run
# create_rois, tell the user that.
except IOError, err:
print("Could not load <name>. Try create_rois() or open_atlases()")
raise IOError(err)
def create_rois(atlas, base, legend):
""" Creates ROI masks for from given <atlas> using <base> (a 4d nifit1
file containg all rois. A <legend>.txt file mapping roi codes to
names is also needed, formatted as 1:Hippocampus. """
# setup pathing, read in the process the base
path = os.path.join(roi.__path__[0], 'atlases')
loni = read_nifti(os.path.join(path, atlas, base))
# Need these for writing the rois out later
header = loni.get_header()
affline = loni.get_affine()
data = loni.get_data()
# And get then the txt file that is its legend.
fhandle = open(os.path.join(path, legend))
fdata = [line.strip().split(':') for line in fhandle]
# Store the legend data in a dict keyed
# on the ROI names.
legend_dict = {}
for col1, col2 in fdata:
legend_dict.update({col2 : int(col1)})
# Loop over the legend, creating and
# saving a nii file for each item.
roi_path = os.path.join(path, atlas, 'rois')
if not os.path.exists(roi_path):
os.mkdir(roi_path)
for key, val in legend_dict.items():
# Mask based on v, the index for he current
# roi then create the binary roi.
mask = np.zeros(data.shape, dtype=np.uint8)
## nifti1 needs unsigned integers
mask[data == val] = 1
# Finally, create a nifti object and write
# it using the key from legend as a name.
niftiname = key + '.nii'
nifti = nb.Nifti1Image(mask, affline, header)
nifti.update_header()
## Not sure this does anything,
## but just in case
write_nifti(nifti, os.path.join(path, atlas, 'rois', niftiname))
def create_rois(atlas, base, legend):
""" Creates ROI masks for from given <atlas> using <base> (a 4d nifit1
file containg all rois. A <legend>.txt file mapping roi codes to
names is also needed, formatted as 1:Hippocampus. """
# setup pathing, read in the process the base
path = os.path.join(roi.__path__[0], 'atlases')
loni = read_nifti(os.path.join(path, atlas, base))
# Need these for writing the rois out later
header = loni.get_header()
affline = loni.get_affine()
data = loni.get_data()
# And get then the txt file that is its legend.
fhandle = open(os.path.join(path, legend))
fdata = [line.strip().split(':') for line in fhandle]
# Store the legend data in a dict keyed
# on the ROI names.
legend_dict = {}
for col1, col2 in fdata:
legend_dict.update({col2: int(col1)})
# Loop over the legend, creating and
# saving a nii file for each item.
roi_path = os.path.join(path, atlas, 'rois')
if not os.path.exists(roi_path):
os.mkdir(roi_path)
for key, val in legend_dict.items():
# Mask based on v, the index for he current
# roi then create the binary roi.
mask = np.zeros(data.shape, dtype=np.uint8)
## nifti1 needs unsigned integers
mask[data == val] = 1
# Finally, create a nifti object and write
# it using the key from legend as a name.
niftiname = key + '.nii'
nifti = nb.Nifti1Image(mask, affline, header)
nifti.update_header()
## Not sure this does anything,
## but just in case
write_nifti(nifti, os.path.join(path, atlas, 'rois', niftiname))
"""Combine ar* functional data in along their 4th axes.
usage: combined_func_biasbox datadir
"""
import sys
import os
from roi.pre import combine4d
from roi.io import read_nifti, write_nifti
# Process the argv
if len(sys.argv[1:]) != 1:
raise ValueError('Only one argument allowed')
datadir = sys.argv[1]
# Name the names, then read in the data
fnames = [
"warbiasbox0.nii", "warbiasbox1.nii", "warbiasbox2.nii", "warbiasbox3.nii",
"warbiasbox4.nii"
]
for i, fname in enumerate(fnames):
if not os.path.exists(os.path.join(datadir, fname)):
print("Missing {0}".format(fname))
fnames.pop(i)
niftis = [read_nifti(os.path.join(datadir, fname)) for fname in fnames]
# Combine the nifti objects and write the result
write_nifti(combine4d(niftis), os.path.join(datadir, "warbiasbox.nii"))
"""
import sys
import os
from roi.pre import combine4d
from roi.io import read_nifti, write_nifti
# Process the argv
if len(sys.argv[1:]) != 1:
raise ValueError('Only one argument allowed')
datadir = sys.argv[1]
# Name the names, then read in the data
fnames = ["warpolygon0.nii",
"warpolygon1.nii",
"warpolygon2.nii",
"warpolygon3.nii",
"warpolygon4.nii",
"warpolygon5.nii"]
# Create the niftis, remove and arn if they do not exist
for i, fname in enumerate(fnames):
if not os.path.exists(os.path.join(datadir, fname)):
print("Missing {0}".format(fname))
fnames.pop(i)
niftis = [read_nifti(os.path.join(datadir, fname)) for fname in fnames]
# Combine the nifti objects and write the result
write_nifti(combine4d(niftis),
os.path.join(datadir, "warpolygon.nii"))
# Process the argv
if len(sys.argv[1:]) != 1:
raise ValueError('Only one argument allowed')
datadir = sys.argv[1]
# Name the names, then read in the data
fnames = [
"warbutterfly0.nii", "warbutterfly1.nii", "warbutterfly2.nii",
"warbutterfly3.nii", "warbutterfly4.nii", "warbutterfly5.nii",
"warbutterfly6.nii", "warbutterfly7.nii", "warbutterfly8.nii",
"warbutterfly9.nii"
]
for i, fname in enumerate(fnames):
if not os.path.exists(os.path.join(datadir, fname)):
print("Missing {0}".format(fname))
fnames.pop(i)
# Create the niftis, remove and arn if they do not exist
niftis = []
for fname in fnames:
try:
niftis.append(read_nifti(os.path.join(datadir, fname)))
except IOError:
print("Warning: {0} not found".format(fname))
pass
#niftis = [read_nifti(os.path.join(datadir, fname)) for fname in fnames]
# Combine the nifti objects and write the result
write_nifti(combine4d(niftis), os.path.join(datadir, "warbutterfly.nii"))
fnames = [
"warbutterfly0.nii",
"warbutterfly1.nii",
"warbutterfly2.nii",
"warbutterfly3.nii",
"warbutterfly4.nii",
"warbutterfly5.nii",
"warbutterfly6.nii",
"warbutterfly7.nii",
"warbutterfly8.nii",
"warbutterfly9.nii"]
for i, fname in enumerate(fnames):
if not os.path.exists(os.path.join(datadir, fname)):
print("Missing {0}".format(fname))
fnames.pop(i)
# Create the niftis, remove and arn if they do not exist
niftis = []
for fname in fnames:
try:
niftis.append(read_nifti(os.path.join(datadir, fname)))
except IOError:
print("Warning: {0} not found".format(fname))
pass
#niftis = [read_nifti(os.path.join(datadir, fname)) for fname in fnames]
# Combine the nifti objects and write the result
write_nifti(combine4d(niftis),
os.path.join(datadir, "warbutterfly.nii"))