subjects_dir = os.path.join(scratch_folder, "fs_subjects_dir")
script_dir = proj_folder + "/scripts/"
included_subjects = db.get_subjects()
# just test with first one!
sub_new = []
#
for sub in [included_subjects[5]]:
if not os.path.isfile(fs_subjects_dir + "%s/%s_t1.nii.gz" % (sub[:4], sub[:4])):
# this is an example of getting the DICOM files as a list
# sequence_name='t1_mprage_3D_sag'
MR_study = db.get_studies(sub, modality="MR")
if len(MR_study) > 0:
# This is a 2D list with [series_name, series_number]
series = db.get_series(sub, MR_study[0], "MR")
t1 = series["t1_mpr_sag_weakFS"]
t2 = series["t2_tse_sag_HighBW"]
# Change this to be more elegant: check whether any item in series
# matches sequence_name
in_t1 = db.get_files(sub, MR_study[0], "MR", t1)
in_t2 = db.get_files(sub, MR_study[0], "MR", t2)
subj_fname = sub[:4]
sub_new += [sub]
convert_t1 = "mri_convert %s %s_t1.nii.gz" % (in_t1[0], subj_fname)
print(convert_t1)
convert_t2 = "mri_convert %s %s_t2.nii.gz" % (in_t2[0], subj_fname)
print(convert_t2)
scratch_folder = os.path.join(proj_folder, 'scratch/maxfiltered_data/')
subjects_dir = os.path.join(scratch_folder, 'fs_subjects_dir')
script_dir = proj_folder + '/scripts/'
included_subjects = db.get_subjects()
# just test with first one!
included_subjects = included_subjects[-3:]
for sub in included_subjects:
# this is an example of getting the DICOM files as a list
# sequence_name='t1_mprage_3D_sag'
MEG_study = db.get_studies(sub, modality='MEG')
if len(MEG_study) > 0:
# This is a 2D list with [series_name, series_number]
series = db.get_series(sub, MEG_study[0], 'MEG')
series = series["data"] # only use the "data" series for now.
# Change this to be more elegant: check whether any item in series
# matches sequence_name
in_name = db.get_files(sub, MEG_study[0], 'MEG', series)
out_name = "%s_%s_mc_raw_tsss.fif" % (sub[:4], "data")
# print(out_name)
# if len(in_name) > 1:
for j, in_file in enumerate(in_name):
if j == 0:
out_fname = scratch_folder + out_name
else:
out_fname = scratch_folder\
+ out_name[:-4] + "-%d.fif" % j