#maskfile = os.path.join(wdir, 'mask_3mm_left_striatum.nii.gz')
#respfile = os.path.join(wdir, 'shoot_data_3mm_n50.nii.gz')
#covfile = os.path.join(wdir, 'covariates_basic_n50.txt')
#cvfolds = 2
# with test covariates
wdir = '/home/mrstats/andmar/py.sandbox/normative_nimg'
##wdir = '/Users/andre/data/normative_nimg'
maskfile = os.path.join(wdir, 'mask_3mm_left_striatum.nii.gz')
respfile = os.path.join(wdir, 'shoot_data_3mm_n500.nii.gz')
covfile = os.path.join(wdir, 'covariates_basic_n500.txt')
testresp = os.path.join(wdir, 'shoot_data_3mm_last100.nii.gz')
testcov = os.path.join(wdir, 'covariates_basic_last100.txt')
estimate(respfile,
covfile,
maskfile,
testresp=testresp,
testcov=testcov,
alg="rfa") #, configparam=4)
#cvfolds = 2
#wdir = '/home/mrstats/andmar/py.sandbox/normative_hcp'
#filename = os.path.join(wdir, 'tfmri_gambling_cope2.dtseries.nii')
#covfile = os.path.join(wdir, 'ddscores.txt')
#Nfold = 2
#wdir = '/home/mrstats/andmar/py.sandbox/normative_oslo'
#respfile = os.path.join(wdir, 'ICA100_oslo15_v2.txt')
#covfile = os.path.join(wdir, 'cov_oslo15_v2.txt')
#cvfolds = 2
#nispat.normative.estimate(respfile, covfile, cvfolds=cvfolds)
print('Removing existing directory')
shutil.rmtree(test_dir)
os.makedirs(test_dir, exist_ok=True)
test_num, tdir = update_test_counter(0, test_dir)
print("\n")
print(test_num, "Testing basic config (gpr with nii data)...")
print("----------------------------------------------------------------------")
mask_file_nii = os.path.join(data_dir, 'mask3.nii.gz')
resp_file_nii = os.path.join(data_dir, 'resp_n50.nii.gz')
cov_file_nii = os.path.join(data_dir, 'cov_n50.txt')
resp_file_nii_te = os.path.join(data_dir, 'resp_n100.nii.gz')
cov_file_nii_te = os.path.join(data_dir, 'cov_n100.txt')
estimate(cov_file_nii, resp_file_nii, maskfile=mask_file_nii,
testresp = resp_file_nii_te, testcov = cov_file_nii_te)
print(os.getcwd())
save_output(os.getcwd(), tdir)
test_num, tdir = update_test_counter(test_num, test_dir)
print(test_num, "Testing again using the same data under cross-validation")
print("----------------------------------------------------------------------")
estimate(cov_file_nii, resp_file_nii, maskfile = mask_file_nii, cvfolds = 2)
save_output(os.getcwd(), tdir)
test_num, tdir = update_test_counter(test_num, test_dir)
print(test_num, "Test again with txt files. This time using blr...")
print("----------------------------------------------------------------------")
#wdir = '/home/mrstats/andmar/py.sandbox/normative_nimg' ##wdir = '/Users/andre/data/normative_nimg' #maskfile = os.path.join(wdir, 'mask_3mm_left_striatum.nii.gz') #respfile = os.path.join(wdir, 'shoot_data_3mm_n50.nii.gz') #covfile = os.path.join(wdir, 'covariates_basic_n50.txt') #cvfolds = 2 # with test covariates wdir = '/home/mrstats/andmar/py.sandbox/normative_nimg' ##wdir = '/Users/andre/data/normative_nimg' maskfile = os.path.join(wdir, 'mask_3mm_left_striatum.nii.gz') respfile = os.path.join(wdir, 'shoot_data_3mm_n50.nii.gz') covfile = os.path.join(wdir, 'covariates_basic_n50.txt') testresp = os.path.join(wdir, 'shoot_data_3mm_last100.nii.gz') testcov = os.path.join(wdir, 'covariates_basic_last100.txt') estimate(respfile, covfile, maskfile, testresp=testresp, testcov=testcov) #cvfolds = 2 #wdir = '/home/mrstats/andmar/py.sandbox/normative_hcp' #filename = os.path.join(wdir, 'tfmri_gambling_cope2.dtseries.nii') #covfile = os.path.join(wdir, 'ddscores.txt') #Nfold = 2 #wdir = '/home/mrstats/andmar/py.sandbox/normative_oslo' #respfile = os.path.join(wdir, 'ICA100_oslo15_v2.txt') #covfile = os.path.join(wdir, 'cov_oslo15_v2.txt') #cvfolds = 2 #nispat.normative.estimate(respfile, covfile, cvfolds=cvfolds) #wdir = '/home/mrstats/andmar/data/enigma_mdd' #maskfile = None
#maskfile = os.path.join(wdir, 'mask_3mm_left_striatum.nii.gz')
#respfile = os.path.join(wdir, 'shoot_data_3mm_n50.nii.gz')
#covfile = os.path.join(wdir, 'covariates_basic_n50.txt')
#cvfolds = 2
# with test covariates
wdir = '/home/preclineu/andmar/py.sandbox/normative_nimg'
##wdir = '/Users/andre/data/normative_nimg'
maskfile = os.path.join(wdir, 'mask_3mm_left_striatum.nii.gz')
respfile = os.path.join(wdir, 'shoot_data_3mm_n500.nii.gz')
covfile = os.path.join(wdir, 'covariates_basic_n500.txt')
testresp = os.path.join(wdir, 'shoot_data_3mm_last100.nii.gz')
testcov = os.path.join(wdir, 'covariates_basic_last100.txt')
estimate(covfile,
respfile,
maskfile=maskfile,
testresp=testresp,
testcov=testcov,
alg="blr") #, configparam=4)
#cvfolds = 2
#wdir = '/home/mrstats/andmar/py.sandbox/normative_hcp'
#filename = os.path.join(wdir, 'tfmri_gambling_cope2.dtseries.nii')
#covfile = os.path.join(wdir, 'ddscores.txt')
#Nfold = 2
#wdir = '/home/mrstats/andmar/py.sandbox/normative_oslo'
#respfile = os.path.join(wdir, 'ICA100_oslo15_v2.txt')
#covfile = os.path.join(wdir, 'cov_oslo15_v2.txt')
#cvfolds = 2
#nispat.normative.estimate(covfile, respfile, cvfolds=cvfolds)
print(normativedir)
# ################################################################################################
# Primary model
wdir = normativedir
os.chdir(wdir)
# input files and paths
cov_train = os.path.join(normativedir, 'cov_train.txt')
resp_train = os.path.join(normativedir, 'resp_train.txt')
cov_test = os.path.join(normativedir, 'cov_test.txt')
resp_test = os.path.join(normativedir, 'resp_test.txt')
# run normative
estimate(resp_train,
cov_train,
testcov=cov_test,
testresp=resp_test,
cvfolds=None,
alg="gpr")
################################################################################################
# Forward model
wdir = os.path.join(normativedir, 'forward')
os.chdir(wdir)
# input files and paths
cov_train = os.path.join(normativedir, 'cov_train.txt')
resp_train = os.path.join(normativedir, 'resp_train.txt')
cov_test = os.path.join(wdir, 'synth_cov_test.txt')
# run normative
estimate(resp_train,
cov_train,
testcov=cov_test,