def main(argv):
thisContrast = None
debug = False
write = False
roi = "grayMatter"
dstype = "raw"
r = 4 # searchlight radius
try:
opts, args = getopt.getopt(argv, "dwhm:c:b:r", ["mfile=", "contrast=", "debug="])
except getopt.GetoptError:
print "searchlight.py -m <maskfile> -c <contrast> "
sys.exit(2)
for opt, arg in opts:
if opt == "-h":
print "searchlight.py -m <maskfile> -c <contrast> "
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
# elif opt in ("-n", "--niter"):
# n = arg
elif opt in ("-c", "--contrast"):
thisContrast = arg
elif opt in ("-d", "--debug"):
print "debug mode"
debug = True
elif opt in ("-w", "--write"):
write = True
elif opt in ("-r", "--radius"):
r = arg
elif opt in ("-b", "--dstype"):
dstype = arg
if not thisContrast:
print "not a valid contrast... exiting"
sys.exit(1)
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
print "Mask: " + str(roi)
print "Full Model: " + str(thisContrast)
print "Searchlight Radius: " + str(r)
print "Write results: " + str(write)
sg_params = [49, 2]
if debug:
subList = {"LMVPA005": subList["LMVPA005"]}
for s in subList.keys():
runsub(
sub=s,
thisContrast=thisContrast,
r=r,
dstype=dstype,
write=write,
filterLen=sg_params[0],
filterOrd=sg_params[1],
roi=roi,
)
def result_hist(scan, masksize):
paths, subList, contrasts, masks = lmvpa.initpaths(plat)
bfn = os.path.join(paths[0], 'Maps', 'Encoding', scan + '.nii.gz')
f, axarr = plt.subplots(len(masks), sharex=True)
axarr[0].set_title('Model: ' + scan + ' | Mask size: ' + str(masksize))
for i, m in enumerate(masks):
mask = os.path.join(paths[0], 'data', s, 'masks', s + '_' + m + '.nii.gz')
d = fmri_dataset(bfn, mask=mask)
axarr[i].hist(np.mean(d[0].samples,0), bins=30)
axarr[i].axvline(x=np.median(d.samples), color='r')
axarr[i].set_ylabel(m)
def result_hist(scan, masksize):
paths, subList, contrasts, masks = lmvpa.initpaths(plat)
bfn = os.path.join(paths[0], 'Maps', 'Encoding', scan + '.nii.gz')
f, axarr = plt.subplots(len(masks), sharex=True)
axarr[0].set_title('Model: ' + scan + ' | Mask size: ' + str(masksize))
for i, m in enumerate(masks):
mask = os.path.join(paths[0], 'data', s, 'masks',
s + '_' + m + '.nii.gz')
d = fmri_dataset(bfn, mask=mask)
axarr[i].hist(np.mean(d[0].samples, 0), bins=30)
axarr[i].axvline(x=np.median(d.samples), color='r')
axarr[i].set_ylabel(m)
def main(argv):
roi = 'grayMatter'
regs = []
debug=False
write=False
try:
opts, args = getopt.getopt(argv, "dwhm:c:", ["mfile=", "contrast=", "debug=", "write="])
except getopt.GetoptError:
print 'encodingAnalysisV4.py -m <maskfile> -c <contrast> '
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'encodingAnalysisV4.py -m <mask> -c <contrast> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
elif opt in ("-c", "--contrast"):
regs = arg.split(',')
elif opt in ("-d", "--debug"):
print "debug mode"
debug = True
elif opt in ("-w", "--write"):
write = True
if not regs:
print "not a valid contrast... exiting"
sys.exit(1)
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
regstr = '+'.join(regs)
print(regstr)
if 'word2vec' in regs:
regs.remove('word2vec')
for i in np.arange(0, 300):
regs.append('word2vec' + str(i))
if 'random' in regs:
regs.remove('random')
for i in np.arange(0, 302):
regs.append('random' + str(i))
sg_params = [49, 2]
chunklen = 30 # this reflects the length of a complete trial
paramEst = .25 # this much data to be held out for ridge regression parameter estimation
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
logging.basicConfig(level=logging.DEBUG)
alphas = np.logspace(-1, 3, 50)
for s in subList.keys():
runsub(sub=s, thisContrast=regs, thisContrastStr=regstr,
filterLen=sg_params[0], filterOrd=sg_params[1], debug=debug,
paramEst=paramEst, chunklen=chunklen, alphas=alphas, write=write, roi=roi)
def main(argv):
thisContrast = None
debug = False
write = False
roi = 'grayMatter'
dstype='raw'
r = 4 # searchlight radius
try:
opts, args = getopt.getopt(argv, "dwhm:c:b:r", ["mfile=", "contrast=", "debug="])
except getopt.GetoptError:
print 'searchlight.py -m <maskfile> -c <contrast> '
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'searchlight.py -m <maskfile> -c <contrast> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
# elif opt in ("-n", "--niter"):
# n = arg
elif opt in ("-c", "--contrast"):
thisContrast = arg
elif opt in ("-d", "--debug"):
print "debug mode"
debug = True
elif opt in ("-w", "--write"):
write = True
elif opt in ("-r", "--radius"):
r = arg
elif opt in ("-b", "--dstype"):
dstype = arg
if not thisContrast:
print "not a valid contrast... exiting"
sys.exit(1)
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
print "Mask: " + str(roi)
print "Full Model: " + str(thisContrast)
print "Searchlight Radius: " + str(r)
print "Write results: " + str(write)
sg_params = [63, 2]
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
for s in subList.keys():
runsub(sub=s, thisContrast=thisContrast, r=r, dstype=dstype, write=write,
filterLen=sg_params[0], filterOrd=sg_params[1], roi=roi)
def main(argv):
roi = 'grayMatter'
thisContrast = []
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
try:
opts, args = getopt.getopt(argv, "hm:c:", ["mfile=", "contrast="])
except getopt.GetoptError:
print 'linearEncoding.py -r <roi> -m <maskfile> -c <contrast> '
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'linearEncoding.py -m <mask> -c <contrast> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
elif opt in ("-c", "--contrast"):
thisContrast = arg.split(',')
debug = False
if not thisContrast:
print "not a valid contrast... exiting"
sys.exit(1)
thisContrastStr = '+'.join(thisContrast)
print(thisContrastStr)
if 'word2vec' in thisContrast:
thisContrast.remove('word2vec')
for i in np.arange(0, 300):
thisContrast.append('word2vec' + str(i))
sg_params = [49, 2]
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
# ds_all = lmvpa.loadsubdata(paths, subList, m=roi, c='trial_type')
# motion parameters for all subjects
# events for beta extraction
# add everything as a sample attribute
for s in subList.keys():
runsub(sub=s,
thisContrast=thisContrast,
thisContrastStr=thisContrastStr,
filterLen=sg_params[0],
filterOrd=sg_params[1],
roi='grayMatter')
def main(argv):
roi = 'grayMatter'
thisContrast = []
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
try:
opts, args = getopt.getopt(argv, "hm:c:", ["mfile=", "contrast="])
except getopt.GetoptError:
print 'linearEncoding.py -r <roi> -m <maskfile> -c <contrast> '
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'linearEncoding.py -m <mask> -c <contrast> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
elif opt in ("-c", "--contrast"):
thisContrast = arg.split(',')
debug=False
if not thisContrast:
print "not a valid contrast... exiting"
sys.exit(1)
thisContrastStr = '+'.join(thisContrast)
print(thisContrastStr)
if 'word2vec' in thisContrast:
thisContrast.remove('word2vec')
for i in np.arange(0, 300):
thisContrast.append('word2vec' + str(i))
sg_params = [49, 2]
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
# ds_all = lmvpa.loadsubdata(paths, subList, m=roi, c='trial_type')
# motion parameters for all subjects
# events for beta extraction
# add everything as a sample attribute
for s in subList.keys():
runsub(sub=s, thisContrast=thisContrast, thisContrastStr=thisContrastStr,
filterLen=sg_params[0], filterOrd=sg_params[1], roi='grayMatter')
# plat = 'mac'
sys.path.append('/Users/njchiang/GitHub/LanguageMVPA/multivariate/python/analysis')
sys.path.append('/Users/njchiang/GitHub/python-fmri-utils/utils')
debug = True
else:
plat = 'win'
sys.path.append('D:\\GitHub\\LanguageMVPA\\multivariate\\python\\analysis')
sys.path.append('D:\\GitHub\\python-fmri-utils\\utils')
debug = False
import lmvpautils as lmvpa
from sklearn import linear_model as lm
from mvpa2.clfs.skl import SKLLearnerAdapter
from mvpa2.clfs import svm
# debug = True
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
import numpy as np
import os
from mvpa2.datasets.mri import map2nifti
from mvpa2.mappers.zscore import zscore
import SavGolFilter as sg
import mvpa2.datasets.eventrelated as er
from mvpa2.measures.base import CrossValidation
from mvpa2.generators.partition import NFoldPartitioner
import searchlightutils as sl
# for sub in subList.keys():
def runsub(sub, thisContrast, r, dstype='raw', roi='grayMatter', filterLen=49, filterOrd=3, write=False):
# plat = 'mac'
sys.path.append('/Users/njchiang/GitHub/LanguageMVPA/multivariate/python/analysis')
sys.path.append('/Users/njchiang/GitHub/python-fmri-utils/utils')
debug = True
else:
plat = 'win'
sys.path.append('D:\\GitHub\\LanguageMVPA\\multivariate\\python\\analysis')
sys.path.append('D:\\GitHub\\python-fmri-utils\\utils')
debug = False
import os
print "Initializing..."
# initialize paths
import lmvpautils as lmvpa
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
# nVox = 100
# initialize subjects, masks, contrast
roi = "left_IFG_operc"
con = "syntax"
chance = .25
dsType = "Lang"
nVox = 500
# dsType = "Pic"
cname = 'LinearSVM'
from mvpa2.clfs import svm
clf = svm.LinearCSVMC()
preproc = 'None'
# feature selection
# preproc = 'fsel-'+str(nVox)
def main(argv):
roi = 'grayMatter'
thisContrast = []
testContrast = []
debug=False
write=False
n = 100
alphas = [1, 2.69, 2.62] # 1.68, 3.56]
try:
opts, args = getopt.getopt(argv, "dwhm:c:t:a", ["mfile=", "contrast=", "test=", "alpha=", "debug="])
except getopt.GetoptError:
print 'encodingAnalysisV5.py -m <maskfile> -c <contrast> -t <testcontrasts> -a <alphas>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'encodingAnalysisV5.py -m <maskfile> -c <contrast> -t <testcontrasts> -a <alphas> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
# elif opt in ("-n", "--niter"):
# n = arg
elif opt in ("-c", "--contrast"):
thisContrast = arg.split(',')
elif opt in ("-t", "--test"):
tmp = arg.split(',')
testContrast.append(tmp)
elif opt in ("-a", "--alpha"):
tmp = arg.split(',')
alphas = [float(i) for i in tmp]
elif opt in ("-d", "--debug"):
print "debug mode"
debug = True
elif opt in ("-w", "--write"):
write = True
if not thisContrast:
print "not a valid contrast... exiting"
sys.exit(1)
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
print "Mask: " + str(roi)
print "Full Model: " + str(thisContrast)
print "Model test: " + str(testContrast)
print "Alphas: " + str(alphas)
thisContrastStr = '+'.join(thisContrast)
print(thisContrastStr)
if 'word2vec' in thisContrast:
thisContrast.remove('word2vec')
for i in np.arange(0, 300):
thisContrast.append('word2vec' + str(i))
if 'random' in thisContrast:
thisContrast.remove('random')
for i in np.arange(0, 302):
thisContrast.append('random' + str(i))
sg_params = [49, 2]
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
logging.basicConfig(level=logging.DEBUG)
for s in subList.keys():
runsub(sub=s, thisContrast=thisContrast, thisContrastStr=thisContrastStr, debug=debug, write=write,
testContrast=testContrast, filterLen=sg_params[0], filterOrd=sg_params[1],
alphas=alphas, roi=roi)
def main(argv):
roi = 'grayMatter'
thisContrast = []
testContrast = []
debug=False
write=False
n = 100
alphas = [1, 2.69, 2.62] # 1.68, 3.56]
try:
opts, args = getopt.getopt(argv, "dwhm:c:t:a", ["mfile=", "contrast=", "test=", "alpha=", "debug="])
except getopt.GetoptError:
print 'encodingAnalysisV5.py -m <maskfile> -c <contrast> -t <testcontrasts> -a <alphas>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'encodingAnalysisV5.py -m <maskfile> -c <contrast> -t <testcontrasts> -a <alphas> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
# elif opt in ("-n", "--niter"):
# n = arg
elif opt in ("-c", "--contrast"):
thisContrast = arg.split(',')
elif opt in ("-t", "--test"):
tmp = arg.split(',')
testContrast.append(tmp)
elif opt in ("-a", "--alpha"):
tmp = arg.split(',')
alphas = [float(i) for i in tmp]
elif opt in ("-d", "--debug"):
print "debug mode"
debug = True
elif opt in ("-w", "--write"):
write = True
if not thisContrast:
print "not a valid contrast... exiting"
sys.exit(1)
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
print "Mask: " + str(roi)
print "Full Model: " + str(thisContrast)
print "Model test: " + str(testContrast)
print "Alphas: " + str(alphas)
thisContrastStr = '+'.join(thisContrast)
print(thisContrastStr)
if 'word2vec' in thisContrast:
thisContrast.remove('word2vec')
for i in np.arange(0, 300):
thisContrast.append('word2vec' + str(i))
if 'random' in thisContrast:
thisContrast.remove('random')
for i in np.arange(0, 302):
thisContrast.append('random' + str(i))
sg_params = [49, 2]
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
logging.basicConfig(level=logging.DEBUG)
for s in subList.keys():
runsub(sub=s, thisContrast=thisContrast, thisContrastStr=thisContrastStr, debug=debug, write=write,
testContrast=testContrast, filterLen=sg_params[0], filterOrd=sg_params[1],
alphas=alphas, roi=roi)
def main(argv):
roi = 'grayMatter'
regs = []
debug = False
write = False
try:
opts, args = getopt.getopt(argv, "dwhm:c:",
["mfile=", "contrast=", "debug=", "write="])
except getopt.GetoptError:
print 'encodingAnalysisV4.py -m <maskfile> -c <contrast> '
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'encodingAnalysisV4.py -m <mask> -c <contrast> '
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
elif opt in ("-c", "--contrast"):
regs = arg.split(',')
elif opt in ("-d", "--debug"):
print "debug mode"
debug = True
elif opt in ("-w", "--write"):
write = True
if not regs:
print "not a valid contrast... exiting"
sys.exit(1)
paths, subList, contrasts, maskList = lmvpa.initpaths(plat)
regstr = '+'.join(regs)
print(regstr)
if 'word2vec' in regs:
regs.remove('word2vec')
for i in np.arange(0, 300):
regs.append('word2vec' + str(i))
if 'random' in regs:
regs.remove('random')
for i in np.arange(0, 302):
regs.append('random' + str(i))
sg_params = [49, 2]
chunklen = 30 # this reflects the length of a complete trial
paramEst = .25 # this much data to be held out for ridge regression parameter estimation
if debug:
subList = {'LMVPA005': subList['LMVPA005']}
logging.basicConfig(level=logging.DEBUG)
alphas = np.logspace(-1, 3, 50)
for s in subList.keys():
runsub(sub=s,
thisContrast=regs,
thisContrastStr=regstr,
filterLen=sg_params[0],
filterOrd=sg_params[1],
debug=debug,
paramEst=paramEst,
chunklen=chunklen,
alphas=alphas,
write=write,
roi=roi)