args = parser.parse_args()
params = vars(args)
json_file = str(params["f"][0])
subj_index = params["n"]
print(json_file)
# read the pipeline params
with open(json_file) as pipeline_file:
pipeline_params = json.load(pipeline_file)
raw_path = pipeline_params["RAW_PATH"]
t1_path = pipeline_params["T1_PATH"]
fs_path = pipeline_params["FS_PATH"]
raw_subjects = files.get_folders_files(raw_path, wp=False)[0]
raw_subjects.sort()
raw_subj = raw_subjects[subj_index]
raw_subj_dir = op.join(raw_path, raw_subj, "scans", "2_t1_mprage_sag_iso_1mm")
t1_subj_dir = op.join(t1_path, raw_subj)
files.make_folder(t1_subj_dir)
def dcm2nii_func(t1_subj_dir, raw_subj_dir):
dcm2nii = "/cubric/software/mricron/dcm2nii"
try:
t1_file = files.get_files(t1_subj_dir, "co", "nii.gz")[2][0]
parser.add_argument("-n", type=int, help="id list index")
args = parser.parse_args()
params = vars(args)
json_file = params["f"]
subj_index = params["n"]
# read the pipeline params
with open(json_file) as pipeline_file:
pipeline_params = json.load(pipeline_file)
# paths
data_path = pipeline_params["data_path"]
fs_path = op.join(data_path, "MRI")
subjs = files.get_folders_files(fs_path, wp=False)[0]
subjs.sort()
subjs = [i for i in subjs if "fsaverage" not in i]
subj = subjs[subj_index]
meg_subj_path = op.join(data_path, "MEG", subj)
beh_subj_path = op.join(data_path, "BEH", subj)
verb = False
if pipeline_params["downsample_convert_filter"]:
raw_ds = files.get_folders_files(meg_subj_path, wp=True)[0]
raw_ds = [i for i in raw_ds if ".ds" in i]
for ix, raw_path in enumerate(raw_ds):
raw = mne.io.read_raw_ctf(raw_path, preload=True, verbose=False)
json_file = sys.argv[2]
print(json_file)
except:
json_file = "pipeline_params.json"
print(json_file)
# open json file
with open(json_file) as pipeline_file:
parameters = json.load(pipeline_file)
# prepare paths
data_path = parameters["path"]
subjects_dir = parameters["freesurfer"]
# subjects
subjs = files.get_folders_files(subjects_dir, wp=False)[0]
subjs = [i for i in subjs if "00" in i]
subjs.sort()
subj = subjs[subj_index]
# processing parameters
down_freq = parameters["downsample"]
chpi = [
"HLC0011", "HLC0012", "HLC0013", "HLC0021", "HLC0022", "HLC0023",
"HLC0031", "HLC0032", "HLC0033"
]
subj_path = op.join(data_path, "MEG", subj)
if parameters["convert_downsample_filter"]:
all_ds = files.get_folders_files(subj_path, wp=True)[0]
try:
file_index = int(sys.argv[2])
except:
print("incorrect file index")
sys.exit()
# open json file
with open(json_file) as pipeline_file:
parameters = json.load(pipeline_file)
# prepare paths
data_path = parameters["path"]
subjects_dir = parameters["freesurfer"]
subjects = files.get_folders_files(subjects_dir, wp=False)[0]
subjects.sort()
subjects = [i for i in subjects if "fsaverage" not in i]
subject = subjects[subj_index]
subject_meg = op.join(data_path, "MEG", subject, parameters["folder"])
raw_paths = files.get_files(subject_meg, "80-", "-raw.fif", wp=True)[2]
raw_paths.sort()
raw_path = raw_paths[file_index]
print(raw_path)
print(subject)
mne.gui.coregistration(subjects_dir=subjects_dir,
subject=subject,
try:
file_index = int(sys.argv[1])
except:
print("incorrect arguments")
sys.exit()
output_path = "/cubric/scratch/c1557187/stirring/RESULTS/SVC/data"
beh_path = "/cubric/scratch/c1557187/stirring/BEH"
beh_files = files.get_files(beh_path, "", "matched.gz")[2]
beh_files.sort()
epo_path = "/cubric/scratch/c1557187/stirring/MEG"
subjects = files.get_folders_files(epo_path, wp=False)[0]
subjects.sort()
long_files = [
files.get_files(op.join(epo_path, i), "long", "epo.fif")[2][0]
for i in subjects
]
long_files.sort()
engage_files = [
files.get_files(op.join(epo_path, i), "engage", "epo.fif")[2][0]
for i in subjects
]
engage_files.sort()
change_files = [
args = parser.parse_args()
params = vars(args)
subj_index = params["n"]
file_index = params["f"]
json_ICA = "ICA_comp.json"
json_file = "pipeline_params.json"
# read the pipeline params
with open(json_file) as pipeline_file:
pipeline_params = json.load(pipeline_file)
# PATHS
data_out = op.join(pipeline_params["output_path"], "data")
subjs = files.get_folders_files(data_out, wp=False)[0]
subjs.sort()
subj = subjs[subj_index]
subj_path = op.join(data_out, subj)
ica_files = files.get_files(subj_path, "", "-ica.fif")[2]
ica_files.sort()
raw_files = files.get_files(subj_path, "", "-raw.fif", wp=True)[2]
raw_files.sort()
raw_file = raw_files[file_index]
ica_file = ica_files[file_index]
try:
json_file = sys.argv[2]
print(json_file)
except:
json_file = "pipeline.json"
print(json_file)
# open json file
with open(json_file) as pipeline_file:
parameters = json.load(pipeline_file)
# prepare paths
data_path = parameters["path"]
subjects_dir = parameters["freesurfer"]
subjects = files.get_folders_files(subjects_dir, wp=False)[0]
subjects.sort()
subjects = [i for i in subjects if "fsaverage" not in i]
subject = subjects[subj_index]
print("subject:", subject)
subject_raw = op.join(data_path, "MEG", subject)
subject_meg = op.join(data_path, "MEG", subject, parameters["folder"])
files.make_folder(subject_meg)
subject_beh = {data_path, "BEH", subject}
if parameters["step_1"]:
