def load_surf_files(nii_fname, run_fmri_preproc=True, user_fol='', debug=True):
fmri_file_template = ''
if user_fol == '':
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
if debug:
print('load_surf_files: nii_fol: {}'.format(nii_fol))
hemi, fmri_hemis = mu.get_hemi_from_full_fname(nii_fname)
if debug:
print('load_surf_files: hemi, fmri_hemis: {}, {}'.format(
hemi, fmri_hemis))
if hemi == '':
hemi = mu.find_hemi_using_vertices_num(nii_fname)
if hemi == '':
return ''
# fmri_hemis = mu.get_both_hemis_files(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
if debug:
print('load_surf_files: local_fname: {}'.format(local_fname))
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
if debug:
print('load_surf_files: other_hemi: {}'.format(other_hemi))
other_hemi_fname = fmri_hemis[other_hemi]
if other_hemi_fname == '':
other_hemi_fname = local_fname.replace(hemi, other_hemi)
if debug:
print('load_surf_files: other_hemi_fname: {}'.format(other_hemi_fname))
# todo: if the other hemi file doens't exist, just create an empty one
output_fname_template = ''
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(
mu.namebase_with_ext(local_fname))
if run_fmri_preproc:
mu.add_mmvt_code_root_to_path()
from src.preproc import fMRI
importlib.reload(fMRI)
vertices_num = mu.get_vertices_num()
ret, npy_output_fname_template = fMRI.load_surf_files(
mu.get_user(), fmri_hemis, vertices_num=vertices_num)
output_fname_template = op.join(
mu.get_parent_fol(npy_output_fname_template),
mu.namebase_with_ext(npy_output_fname_template)[len('fmri_'):])
else:
mu.run_mmvt_func(
'src.preproc.fMRI',
'load_surf_files',
flags='--fmri_file_template "{}"'.format(fmri_file_template))
# todo: find what should be the output_fname_template
else:
print(
"Couldn't find the other hemi file! ({})".format(other_hemi_fname))
return output_fname_template #, hemi, other_hemi
def load_surf_files(nii_fname):
fmri_file_template = ''
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
fmri_hemis = mu.get_both_hemis_files(nii_fname)
hemi = mu.get_hemi_from_full_fname(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
other_hemi_fname = fmri_hemis[other_hemi]
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(mu.namesbase_with_ext(local_fname))
cmd = '{} -m src.preproc.fMRI -s {} -f load_surf_files --fmri_file_template "{}"'.format(
bpy.context.scene.python_cmd, mu.get_user(), fmri_file_template)
mu.run_command_in_new_thread(cmd, False)
return fmri_file_template, hemi
def load_surf_files(nii_fname, run_fmri_preproc=True, user_fol=''):
fmri_file_template = ''
if user_fol == '':
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
# hemi = mu.get_hemi_from_fname(mu.namebase(nii_fname))
# if hemi == '':
hemi, fmri_hemis = mu.get_hemi_from_full_fname(nii_fname)
if hemi == '':
hemi = mu.find_hemi_using_vertices_num(nii_fname)
if hemi == '':
return '', ''
# fmri_hemis = mu.get_both_hemis_files(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
other_hemi_fname = fmri_hemis[other_hemi]
# todo: if the other hemi file doens't exist, just create an empty one
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(
mu.namebase_with_ext(local_fname))
if run_fmri_preproc:
mu.run_mmvt_func(
'src.preproc.fMRI',
'load_surf_files',
flags='--fmri_file_template "{}"'.format(fmri_file_template))
# cmd = '{} -m -s {} -f --fmri_file_template "{}" --ignore_missing 1'.format(
# bpy.context.scene.python_cmd, mu.get_user(), fmri_file_template)
# mu.run_command_in_new_thread(cmd, False, cwd=mu.get_mmvt_code_root())
else:
print(
"Couldn't find the other hemi file! ({})".format(other_hemi_fname))
return fmri_file_template, hemi, other_hemi