def create(mask, path, niipartial, newname, restart=False):
"""Create a roi dataset using all Ploran 2007 (i.e. butterfly)
datasets.
Input
-----
mask - name of a roi found in the Harvard Oxford atlas (see roi
package for details)
path - the base path where all the BOLD data lives
niipartial - a string the matches all data of interest
newname - a name for all the combined roi data. Note: all roi data is
saved in ./roinii/
"""
try:
os.mkdir("./roinii")
except OSError:
pass
# Get and order the nii files
print("Finding nii files.")
niis = findallnii(path, niipartial)
niis, bysub = _ordernii_butterfly(niis)
# Mask and combine
roinames = {}
for sub in sorted(bysub.keys()):
roinames[sub] = []
for scan in bysub[sub]:
if scan != None:
roiname = _mask_butterfly(mask, scan, newname, restart)
roinames[sub].append(roiname)
else:
roinames[sub].append(None)
print("Combining all roi data by subject.")
for sub, scans in roinames.items():
scans = [scan for scan in scans if scan != None]
## Drop None
# Init combinedniis then add the
# remaining scans to it and save
# the result
print("Combining {0}.".format(sub))
combinedniis = nb.load(scans.pop(0))
for scan in scans:
combinedniis = join_time(combinedniis, nb.load(scan))
print("Saving {0}.".format(sub))
nb.save(combinedniis,
os.path.join(
"./roinii", "{0}_{1}.nii.gz".format(newname, sub)))
def create(mask, path, niipartial, newname, restart=False):
"""Create a roi dataset using all Ploran 2007 (i.e. butterfly)
datasets.
Input
-----
mask - name of a roi found in the Harvard Oxford atlas (see roi
package for details)
path - the base path where all the BOLD data lives
niipartial - a string the matches all data of interest
newname - a name for all the combined roi data. Note: all roi data is
saved in ./roinii/
"""
try:
os.mkdir("./roinii")
except OSError:
pass
# Get and order the nii files
print("Finding nii files.")
niis = findallnii(path, niipartial)
niis, bysub = _ordernii_butterfly(niis)
# Mask and combine
roinames = {}
for sub in sorted(bysub.keys()):
roinames[sub] = []
for scan in bysub[sub]:
if scan != None:
roiname = _mask_butterfly(mask, scan, newname, restart)
roinames[sub].append(roiname)
else:
roinames[sub].append(None)
print("Combining all roi data by subject.")
for sub, scans in roinames.items():
scans = [scan for scan in scans if scan != None]
## Drop None
# Init combinedniis then add the
# remaining scans to it and save
# the result
print("Combining {0}.".format(sub))
combinedniis = nb.load(scans.pop(0))
for scan in scans:
combinedniis = join_time(combinedniis, nb.load(scan))
print("Saving {0}.".format(sub))
nb.save(
combinedniis,
os.path.join("./roinii", "{0}_{1}.nii.gz".format(newname, sub)))
def create(args):
"""Create a roi dataset using all Ploran 2007 (i.e. butterfly)
datasets.
Input
-----
mask - name of a roi found in the Harvard Oxford atlas (see roi
package for details)
path - the base path where all the BOLD data lives
niipartial - a string the matches all data of interest
newname - a name for all the combined roi data. Note: all roi data is
saved in ./roinii/
"""
# Process args, a dunmb way to make this function
# compatible with pool.map()
mask = args[0]
path = args[1]
niipartial = args[2]
newname = args[3]
restart = args[4]
try:
os.mkdir("./roinii")
except OSError:
pass
# Get and order the nii files
print("Finding nii files.")
niis = findallnii(path, niipartial)
niis, bysub = _ordernii_butterfly(niis)
# Mask and combine
roinames = {}
for sub in sorted(bysub.keys()):
roinames[sub] = []
for scan in bysub[sub]:
if scan != None:
roiname = _mask_butterfly(mask, scan, newname, restart)
roinames[sub].append(roiname)
else:
roinames[sub].append(None)
print("Combining all roi data by subject.")
for sub, scans in roinames.items():
scans = [scan for scan in scans if scan != None]
## Drop None
# Init combinedniis then add the
# remaining scans to it and save
# the result
print("Combining {0}.".format(sub))
combinedniis = nb.load(scans.pop(0))
cname = os.path.join(
"./roinii", "{0}_{1}.nii.gz".format(newname, sub))
# If the combinedniis exists, move on (if we're
# in restart mode)
if restart and os.path.isfile(cname):
print("{0} exists, continuing on.".format(cname))
else:
for scan in scans:
combinedniis = join_time(combinedniis, nb.load(scan))
print("Saving {0}.".format(sub))
nb.save(combinedniis, cname)
def create(args):
"""Create a roi dataset using all Ploran 2007 (i.e. butterfly)
datasets.
Input
-----
mask - name of a roi found in the Harvard Oxford atlas (see roi
package for details)
path - the base path where all the BOLD data lives
niipartial - a string the matches all data of interest
newname - a name for all the combined roi data. Note: all roi data is
saved in ./roinii/
"""
# Process args, a dunmb way to make this function
# compatible with pool.map()
mask = args[0]
path = args[1]
niipartial = args[2]
newname = args[3]
restart = args[4]
try:
os.mkdir("./roinii")
except OSError:
pass
# Get and order the nii files
print("Finding nii files.")
niis = findallnii(path, niipartial)
niis, bysub = _ordernii_butterfly(niis)
# Mask and combine
roinames = {}
for sub in sorted(bysub.keys()):
roinames[sub] = []
for scan in bysub[sub]:
if scan != None:
roiname = _mask_butterfly(mask, scan, newname, restart)
roinames[sub].append(roiname)
else:
roinames[sub].append(None)
print("Combining all roi data by subject.")
for sub, scans in roinames.items():
scans = [scan for scan in scans if scan != None]
## Drop None
# Init combinedniis then add the
# remaining scans to it and save
# the result
print("Combining {0}.".format(sub))
combinedniis = nb.load(scans.pop(0))
cname = os.path.join("./roinii", "{0}_{1}.nii.gz".format(newname, sub))
# If the combinedniis exists, move on (if we're
# in restart mode)
if restart and os.path.isfile(cname):
print("{0} exists, continuing on.".format(cname))
else:
for scan in scans:
combinedniis = join_time(combinedniis, nb.load(scan))
print("Saving {0}.".format(sub))
nb.save(combinedniis, cname)
