def save_labels_from_vertices_lookup(subject,
atlas,
subjects_dir,
mmvt_dir,
surf_type='pial',
read_labels_from_fol='',
overwrite_vertices_labels_lookup=False,
n_jobs=6):
lookup = create_vertices_labels_lookup(
subject,
atlas,
read_labels_from_fol=read_labels_from_fol,
overwrite=overwrite_vertices_labels_lookup)
labels_fol = op.join(subjects_dir, subject, 'label', atlas)
surf = utils.load_surf(subject, mmvt_dir, subjects_dir)
utils.delete_folder_files(labels_fol)
ok = True
for hemi in utils.HEMIS:
labels_vertices = defaultdict(list)
# surf_fname = op.join(subjects_dir, subject, 'surf', '{}.{}'.format(hemi, surf_type))
# surf, _ = mne.surface.read_surface(surf_fname)
for vertice, label in lookup[hemi].items():
labels_vertices[label].append(vertice)
chunks_indices = np.array_split(np.arange(len(labels_vertices)),
n_jobs)
labels_vertices_items = list(labels_vertices.items())
chunks = [([labels_vertices_items[ind] for ind in chunk_indices],
subject, labels_vertices, surf, hemi, labels_fol)
for chunk_indices in chunks_indices]
results = utils.run_parallel(_save_labels_from_vertices_lookup_hemi,
chunks, n_jobs)
ok = ok and all(results)
return ok
def subcortical_segmentation(subject, overwrite_subcortical_objs=False):
# Must source freesurfer. You need to have write permissions on SUBJECTS_DIR
script_fname = op.join(BRAINDER_SCRIPTS_DIR, 'aseg2srf')
if not op.isfile(script_fname):
raise Exception('The subcortical segmentation script is missing! {}'.format(script_fname))
if not utils.is_exe(script_fname):
utils.set_exe_permissions(script_fname)
# aseg2srf: For every subcortical region (8 10 11 12 13 16 17 18 26 47 49 50 51 52 53 54 58):
# 1) mri_pretess: Changes region segmentation so that the neighbors of all voxels have a face in common
# 2) mri_tessellate: Creates surface by tessellating
# 3) mris_smooth: Smooth the new surface
# 4) mris_convert: Convert the new surface into srf format
function_output_fol = op.join(SUBJECTS_DIR, subject, 'mmvt', 'subcortical_objs')
renamed_output_fol = op.join(SUBJECTS_DIR, subject, 'mmvt', 'subcortical')
lookup = load_subcortical_lookup_table()
obj_files = glob.glob(op.join(function_output_fol, '*.srf'))
if len(obj_files) < len(lookup) or overwrite_subcortical_objs:
utils.delete_folder_files(function_output_fol)
# utils.delete_folder_files(aseg_to_srf_output_fol)
utils.delete_folder_files(renamed_output_fol)
print('Trying to write into {}'.format(function_output_fol))
utils.run_script(ASEG_TO_SRF.format(subject))
# os.rename(aseg_to_srf_output_fol, function_output_fol)
ply_files = glob.glob(op.join(renamed_output_fol, '*.ply'))
if len(ply_files) < len(lookup) or overwrite_subcortical_objs:
convert_and_rename_subcortical_files(subject, function_output_fol, renamed_output_fol, lookup)
flag_ok = len(glob.glob(op.join(renamed_output_fol, '*.ply'))) == len(lookup) and \
len(glob.glob(op.join(renamed_output_fol, '*.npz'))) == len(lookup)
return flag_ok
def _calc_pvals_fMRI_clusters(p, extract_time_series_for_clusters=False):
subject, overwrite = p
stc_name = 'dSPM_mean_flip_vertices_power_spectrum_stat'
if not utils.both_hemi_files_exist(
op.join(MMVT_DIR, subject, 'meg', '{}-{}.stc'.format(
stc_name, '{hemi}'))):
print('{}: Can\'t find {}!'.format(subject, stc_name))
return False
args.subject = subject
clusters_root_fol = utils.make_dir(
op.join(MMVT_DIR, subject, 'meg', 'clusters'))
res_fname = op.join(
clusters_root_fol,
'clusters_labels_dSPM_mean_flip_vertices_power_spectrum_stat.pkl')
if not op.isfile(res_fname) or args.overwrite:
utils.delete_folder_files(clusters_root_fol)
_args = meg.read_cmd_args(
dict(subject=subject,
mri_subject=subject,
atlas='MSIT_I-C',
function='find_functional_rois_in_stc',
stc_name=stc_name,
threshold=-np.log10(0.01),
threshold_is_precentile=False,
extract_time_series_for_clusters=False,
save_func_labels=True,
calc_cluster_contours=True,
n_jobs=args.n_jobs))
try:
meg.call_main(_args)
except:
print(traceback.format_exc())
if not op.isfile(res_fname):
print('Cluster output can\'t be found!')
return False
def change_frames_names(fol,
images_prefix,
images_type,
images_format_len,
new_fol_name='new_images'):
import shutil
images = glob.glob(
op.join(fol, '{}*.{}'.format(images_prefix, images_type)))
images.sort(key=lambda x: int(utils.namebase(x)[len(images_prefix):]))
images_formats = {
1: '{0:0>1}',
2: '{0:0>2}',
3: '{0:0>3}',
4: '{0:0>4}',
5: '{0:0>5}'
}
root = op.join(op.sep.join(images[0].split(op.sep)[:-1]))
new_fol = op.join(root, new_fol_name)
utils.delete_folder_files(new_fol)
utils.make_dir(new_fol)
for num, image_fname in enumerate(images):
num_str = images_formats[images_format_len].format(num + 1)
new_image_fname = op.join(
new_fol, '{}{}.{}'.format(images_prefix, num_str, images_type))
print('{} -> {}'.format(image_fname, new_image_fname))
utils.copy_file(image_fname, new_image_fname)
return new_fol
def merge_labels(subject, fmri_names):
utils.delete_folder_files(op.join(MMVT_DIR, subject, 'fmri', 'labels'))
vertices_labels_lookup = utils.load(
op.join(MMVT_DIR, subject,
'aparc.DKTatlas40_vertices_labels_lookup.pkl'))
output_fol = utils.make_dir(op.join(MMVT_DIR, subject, 'fmri', 'labels'))
for fmri_name in fmri_names:
labels = []
for hemi in utils.HEMIS:
surf_fname = op.join(
MMVT_DIR, subject, 'fmri', 'fmri_{}_{}.npy'.format(
fmri_name.replace('_insulaopercula', ''), hemi))
surf_data = np.load(surf_fname)
vertices_indices = np.where(surf_data >= 0.95)[0]
if len(vertices_indices) == 0:
continue
insulaopercula_vertices = []
vertices, _ = utils.read_pial(subject, MMVT_DIR, hemi)
for vert_ind in tqdm(vertices_indices):
vert_label = vertices_labels_lookup[hemi][vert_ind]
if vert_label.startswith(
'insula'
): # or vert_label.startswith('parsopercularis')
insulaopercula_vertices.append(vert_ind)
label = mne.Label(insulaopercula_vertices,
vertices[insulaopercula_vertices],
hemi=hemi,
name=fmri_name,
subject=subject)
labels.append(label)
label.save(op.join(output_fol, '{}.label'.format(fmri_name)))
anat.labels_to_annot(subject, atlas=fmri_name, labels=labels)
anat.calc_labeles_contours(subject, fmri_name)
def calc_msit_functional_rois(args):
clusters_root_fol = utils.make_dir(
op.join(MMVT_DIR, args.subject[0], 'meg', 'clusters'))
utils.delete_folder_files(clusters_root_fol)
# conditions = ['neutral', 'interference']
# for cond in conditions:
_args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
data_per_task=True,
# atlas='laus125',
function='find_functional_rois_in_stc',
inverse_method='dSPM',
stc_name=
'{subject}_msit_nTSSS_interference_interference-neutral_1-15-dSPM',
inv_fname='{subject}_msit_nTSSS_interference_1-15-inv',
label_name_template='*',
peak_mode='pos',
threshold=99.5,
min_cluster_max=5,
min_cluster_size=100,
# recreate_src_spacing='ico5'
# clusters_label='precentral'
))
meg.call_main(_args)
def create_dup_frames_links(subject, dup_frames, fol):
fol = op.join(MMVT_DIR, subject, 'figures', fol)
utils.delete_folder_files(fol)
utils.make_dir(fol)
for ind, frame in enumerate(dup_frames):
utils.make_link(
frame, op.join(fol, 'dup_{}.{}'.format(ind,
utils.file_type(frame))))
return fol
def _mri_cvs_register_parallel(p):
subjects, subject_to, subjects_dir, overwrite, print_only = p
for subject_from in subjects:
if overwrite and not print_only:
utils.delete_folder_files(
op.join(subjects_dir, subject_from,
'mri_cvs_register_to_{}'.format(subject_to)))
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mri_cvs_register)
def rename_cortical(lookup, fol, new_fol):
ply_files = glob.glob(op.join(fol, '*.ply'))
utils.delete_folder_files(new_fol)
for ply_file in ply_files:
base_name = op.basename(ply_file)
num = int(base_name.split('.')[-2])
hemi = base_name.split('.')[0]
name = lookup[hemi].get(num, num)
new_name = '{}-{}'.format(name, hemi)
shutil.copy(ply_file, op.join(new_fol, '{}.ply'.format(new_name)))
def rename_cortical(lookup, fol, new_fol):
ply_files = glob.glob(op.join(fol, '*.ply'))
utils.delete_folder_files(new_fol)
for ply_file in ply_files:
base_name = op.basename(ply_file)
num = int(base_name.split('.')[-2])
hemi = base_name.split('.')[0]
name = lookup[hemi].get(num, num)
new_name = '{}-{}'.format(name, hemi)
shutil.copy(ply_file, op.join(new_fol, '{}.ply'.format(new_name)))
def convert_and_rename_subcortical_files(subject, fol, new_fol, lookup, mmvt_subcorticals_fol_name='subcortical'):
obj_files = glob.glob(op.join(fol, '*.srf'))
utils.delete_folder_files(new_fol)
for obj_file in obj_files:
num = int(op.basename(obj_file)[:-4].split('_')[-1])
new_name = lookup.get(num, '')
if new_name != '':
utils.srf2ply(obj_file, op.join(new_fol, '{}.ply'.format(new_name)))
verts, faces = utils.read_ply_file(op.join(new_fol, '{}.ply'.format(new_name)))
np.savez(op.join(new_fol, '{}.npz'.format(new_name)), verts=verts, faces=faces)
copy_subcorticals_to_mmvt(new_fol, subject, mmvt_subcorticals_fol_name)
def convert_and_rename_subcortical_files(subject, fol, new_fol, lookup):
obj_files = glob.glob(op.join(fol, '*.srf'))
utils.delete_folder_files(new_fol)
for obj_file in obj_files:
num = int(op.basename(obj_file)[:-4].split('_')[-1])
new_name = lookup.get(num, '')
if new_name != '':
utils.srf2ply(obj_file, op.join(new_fol, '{}.ply'.format(new_name)))
verts, faces = utils.read_ply_file(op.join(new_fol, '{}.ply'.format(new_name)))
np.savez(op.join(new_fol, '{}.npz'.format(new_name)), verts=verts, faces=faces)
copy_subcorticals_to_blender(new_fol, subject)
def duplicate_frames(fol, multiplier=50, pics_type='png'):
import shutil
pics = get_pics(fol, pics_type)
new_fol = '{}_dup'.format(fol)
utils.delete_folder_files(new_fol)
pic_ind = 0
shutil.copy(op.join(fol, 'data.pkl'), op.join(new_fol, 'data.pkl'))
for t, pic in enumerate(pics):
for _ in range(multiplier):
new_pic_name = op.join(new_fol, '{}_t{}.{}'.format(pic_ind, t, pics_type))
shutil.copy(pic, new_pic_name)
pic_ind += 1
def create_functional_rois(subject, contrast_name, clusters_labels_fname='', func_rois_folder=''):
if clusters_labels_fname == '':
clusters_labels = utils.load(op.join(
BLENDER_ROOT_DIR, subject, 'fmri', 'clusters_labels_{}.npy'.format(contrast_name)))
if func_rois_folder == '':
func_rois_folder = op.join(SUBJECTS_DIR, subject, 'mmvt', 'fmri', 'functional_rois', '{}_labels'.format(contrast_name))
utils.delete_folder_files(func_rois_folder)
for cl in clusters_labels:
cl_name = 'fmri_{}_{:.2f}'.format(cl['name'], cl['max'])
new_label = mne.Label(cl['vertices'], cl['coordinates'], hemi=cl['hemi'], name=cl_name,
filename=None, subject=subject, verbose=None)
new_label.save(op.join(func_rois_folder, cl_name))
def duplicate_frames(fol, multiplier=50, pics_type='png'):
import shutil
pics = get_pics(fol, pics_type)
new_fol = '{}_dup'.format(fol)
utils.delete_folder_files(new_fol)
pic_ind = 0
utils.copy_file(op.join(fol, 'data.pkl'), op.join(new_fol, 'data.pkl'))
for t, pic in enumerate(pics):
for _ in range(multiplier):
new_pic_name = op.join(new_fol, '{}_t{}.{}'.format(pic_ind, t, pics_type))
utils.copy_file(pic, new_pic_name)
pic_ind += 1
def find_functional_rois(subject,
ictal_clips,
modality,
seizure_times,
atlas,
min_cluster_size,
inverse_method,
overwrite=False,
n_jobs=4):
fwd_usingMEG, fwd_usingEEG = meg.get_fwd_flags(modality)
modality_fol = op.join(MMVT_DIR, subject, meg.modality_fol(modality))
stcs_fol = op.join(modality_fol,
'ictal-{}-zvals-stcs'.format(inverse_method))
ictlas_fname = op.join(
modality_fol, '{}-epilepsy-{}-{}-amplitude-zvals-ictals.pkl'.format(
subject, inverse_method, modality))
# Make sure we have a morph map, and if not, create it here, and not in the parallel function
mne.surface.read_morph_map(subject, subject, subjects_dir=SUBJECTS_DIR)
connectivity = anat.load_connectivity(subject)
if overwrite:
utils.delete_folder_files(
op.join(MMVT_DIR, subject, modality_fol, 'clusters'))
if op.isfile(ictlas_fname):
ictals = utils.load(ictlas_fname)
else:
params = [(subject, clip_fname, inverse_method, modality,
seizure_times, stcs_fol, n_jobs)
for clip_fname in ictal_clips]
ictals = utils.run_parallel(_calc_ictal_and_baseline_parallel, params,
n_jobs)
utils.save(ictals, ictlas_fname)
for stc_name, ictal_stc, mean_baseline in ictals:
max_ictal = ictal_stc.data.max()
if max_ictal < mean_baseline:
print('max ictal ({}) < mean baseline ({})!'.format(
max_ictal, mean_baseline))
continue
meg.find_functional_rois_in_stc(subject,
subject,
atlas,
utils.namebase(stc_name),
mean_baseline,
threshold_is_precentile=False,
extract_time_series_for_clusters=False,
time_index=0,
min_cluster_size=min_cluster_size,
min_cluster_max=mean_baseline,
fwd_usingMEG=fwd_usingMEG,
fwd_usingEEG=fwd_usingEEG,
stc_t_smooth=ictal_stc,
modality=modality,
connectivity=connectivity,
n_jobs=n_jobs)
def convert_and_rename_subcortical_files(subject, fol, new_fol, lookup):
obj_files = glob.glob(op.join(fol, '*.srf'))
utils.delete_folder_files(new_fol)
for obj_file in obj_files:
num = int(op.basename(obj_file)[:-4].split('_')[-1])
new_name = lookup.get(num, '')
if new_name != '':
utils.srf2ply(obj_file, op.join(new_fol, '{}.ply'.format(new_name)))
verts, faces = utils.read_ply_file(op.join(new_fol, '{}.ply'.format(new_name)))
np.savez(op.join(new_fol, '{}.npz'.format(new_name)), verts=verts, faces=faces)
blender_fol = op.join(MMVT_DIR, subject, 'subcortical')
if op.isdir(blender_fol):
shutil.rmtree(blender_fol)
shutil.copytree(new_fol, blender_fol)
def find_functional_rois(
subject, ictal_clips, modality, seizure_times, atlas, min_cluster_size, inverse_method, mean_baseline,
windows_length=0.1, windows_shift=0.05, overwrite=False, n_jobs=4):
modality_fol = op.join(MMVT_DIR, subject, meg.modality_fol(modality))
# Make sure we have a morph map, and if not, create it here, and not in the parallel function
mne.surface.read_morph_map(subject, subject, subjects_dir=SUBJECTS_DIR)
connectivity = anat.load_connectivity(subject)
if overwrite:
utils.delete_folder_files(op.join(MMVT_DIR, subject, modality_fol, 'clusters'))
windows = calc_windows(seizure_times, windows_length, windows_shift)
params = []
for ictal_clip in ictal_clips:
for from_t, to_t in windows:
params.append((subject, modality, ictal_clip, atlas, inverse_method, mean_baseline, from_t, to_t,
min_cluster_size, connectivity))
utils.run_parallel(_find_functional_rois_parallel, params, n_jobs)
def find_diff_clusters(subject, atlas='laus125', overwrite=True):
clusters_name = 'CBF_scan_rescan'
if overwrite:
utils.delete_folder_files(op.join(
MMVT_DIR, subject, 'fmri',
'clusters_labels_{}_{}'.format(clusters_name, atlas)),
delete_folder=True)
utils.delete_file(
op.join(MMVT_DIR, subject, 'fmri',
'clusters_labels_{}_{}.pkl'.format(clusters_name, atlas)))
fMRI.find_clusters(subject,
'CBF_scan_rescan',
2,
'laus125',
2,
1,
create_clusters_labels=True,
new_atlas_name='CBF_scan_rescan')
def _mri_cvs_register_parallel(p):
subjects, subject_to, subjects_dir, overwrite, print_only = p
for subject_from in subjects:
# output_fname = op.join(SUBJECTS_DIR, subject_from, 'mri_cvs_register_to_colin27', 'combined_tocolin27_elreg_afteraseg-norm.tm3d')
# if op.isfile(output_fname) and not overwrite:
# print('Already done for {}'.format(subject_from))
# continue
# else:
# print('Running mri_cvs_register for {}'.format(subject_from))
if overwrite and not print_only:
utils.delete_folder_files(
op.join(subjects_dir, subject_from,
'mri_cvs_register_to_{}'.format(subject_to)))
rs = utils.partial_run_script(locals(), print_only=print_only)
if subject_to == 'fsaverage':
rs(mri_cvs_register_mni)
else:
rs(mri_cvs_register)
def calc_contoures(subject,
fmri_names,
thresholds_min=2,
thresholds_max=None,
thresholds_dx=2,
n_jobs=4):
utils.delete_folder_files(op.join(MMVT_DIR, subject, 'fmri', 'clusters'))
if thresholds_max is None:
thresholds_max = thresholds_min
for fmri_name in fmri_names:
fmri.contrast_to_contours(subject,
fmri_name,
thresholds_min,
thresholds_max,
thresholds_dx,
min_cluster_size=10,
find_clusters_overlapped_labeles=True,
atlas='aparc.DKTatlas',
n_jobs=n_jobs)
def calc_functional_rois(conds, args):
clusters_root_fol = op.join(MMVT_DIR, subject, 'meg', 'clusters')
utils.delete_folder_files(clusters_root_fol)
for cond in conds.keys():
_args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
atlas='laus250',
function='find_functional_rois_in_stc',
inverse_method='MNE',
stc_name='{}-MNE-1-15'.format(cond),
label_name_template='precentral*',
inv_fname='{}-inv'.format(cond),
threshold=99.5,
min_cluster_max=0.2,
min_cluster_size=100,
# clusters_label='precentral'
))
meg.call_main(_args)
def recon_all_clin(args):
# python -m src.preproc.examples.anatomy -s nmr01426 -f recon_all_clin --clin_fol clin_6966926 --dicoms_fol Prisma_fit-67026-20200618-141203-000586
import os
for subject, clin_fol, dicoms_fol in zip(args.subject, args.clin_fol,
args.dicoms_fol):
clin_full_fol = utils.make_dir(
op.join(args.clin_root, clin_fol, 'mne_dicom'))
memprage_fols = glob.glob(op.join(clin_full_fol, '*MEMPRAGE*'))
print('mne_organize_dicom output fol: {}'.format(clin_full_fol))
if len(memprage_fols) > 0:
ret = au.is_true(
input(
'It seems like you already have memprage folders, are you sure you want to rerun?'
))
if not ret:
continue
utils.delete_folder_files(clin_full_fol)
fs_dir = utils.make_dir(op.join(args.fs_root, subject))
print('FreeSurfer output fol: {}'.format(fs_dir))
dicoms_full_path = op.join(args.dicoms_root, dicoms_fol)
if not op.isdir(dicoms_full_path):
print('{} does not exist!'.format(dicoms_full_path))
continue
rs = utils.partial_run_script(locals(), print_only=args.print_only)
os.chdir(clin_full_fol)
rs('mne_organize_dicom {dicoms_full_path}')
anat.recon_all(subject,
clin_full_fol,
overwrite=True,
subjects_dir=args.fs_root,
print_only=False,
n_jobs=args.n_jobs)
args = anat.read_cmd_args(
dict(
subject=subject,
function='all,create_skull_surfaces',
remote_subject_dir=op.join(args.fs_root, subject),
n_jobs=args.n_jobs,
))
pu.run_on_subjects(args, anat.main)
def subcortical_segmentation(subject, overwrite_subcorticals=False, model='subcortical', lookup=None,
mask_name='aseg.mgz', mmvt_subcorticals_fol_name='subcortical',
template_subject='', norm_name='norm.mgz', overwrite=True):
# 1) mri_pretess: Changes region segmentation so that the neighbors of all voxels have a face in common
# 2) mri_tessellate: Creates surface by tessellating
# 3) mris_smooth: Smooth the new surface
# 4) mris_convert: Convert the new surface into srf format
template_subject = subject if template_subject == '' else template_subject
norm_fname = op.join(SUBJECTS_DIR, template_subject, 'mri', norm_name)
if not op.isfile(norm_fname):
print('norm file does not exist! {}'.format(norm_fname))
return False
mask_fname = op.join(SUBJECTS_DIR, template_subject, 'mri', mask_name)
if not op.isfile(mask_fname):
print('mask file does not exist! {}'.format(mask_fname))
return False
codes_file = op.join(MMVT_DIR, 'sub_cortical_codes.txt')
if not op.isfile(codes_file):
print('subcortical codes file does not exist! {}'.format(codes_file))
return False
# subcortical_lookup = np.genfromtxt(codes_file, dtype=str, delimiter=',')
function_output_fol = op.join(SUBJECTS_DIR, subject, 'mmvt', '{}_objs'.format(model))
utils.make_dir(function_output_fol)
renamed_output_fol = op.join(SUBJECTS_DIR, subject, 'mmvt', model)
utils.make_dir(renamed_output_fol)
if lookup is None:
lookup = load_subcortical_lookup_table()
obj_files = glob.glob(op.join(function_output_fol, '*.srf'))
errors = []
if len(obj_files) < len(lookup) or overwrite_subcorticals:
if overwrite:
utils.delete_folder_files(function_output_fol)
utils.delete_folder_files(renamed_output_fol)
print('Trying to write into {}'.format(function_output_fol))
for region_id in lookup.keys():
if op.isfile(op.join(function_output_fol, '{}.srf'.format(region_id))):
continue
ret = fu.aseg_to_srf(subject, SUBJECTS_DIR, function_output_fol, region_id, mask_fname, norm_fname,
overwrite_subcorticals)
if not ret:
errors.append(lookup[region_id])
if len(errors) > 0:
print('Errors: {}'.format(','.join(errors)))
ply_files = glob.glob(op.join(renamed_output_fol, '*.ply'))
if len(ply_files) < len(lookup) or overwrite_subcorticals:
convert_and_rename_subcortical_files(subject, function_output_fol, renamed_output_fol, lookup,
mmvt_subcorticals_fol_name)
blender_dir = op.join(MMVT_DIR, subject, mmvt_subcorticals_fol_name)
if not op.isdir(blender_dir) or len(glob.glob(op.join(blender_dir, '*.ply'))) < len(ply_files) or overwrite_subcorticals:
utils.delete_folder_files(blender_dir)
copy_subcorticals_to_mmvt(renamed_output_fol, subject, mmvt_subcorticals_fol_name)
flag_ok = len(glob.glob(op.join(blender_dir, '*.ply'))) >= len(lookup) and \
len(glob.glob(op.join(blender_dir, '*.npz'))) >= len(lookup)
return flag_ok
def create_functional_rois(subject,
contrast_name,
clusters_labels_fname='',
func_rois_folder=''):
if clusters_labels_fname == '':
clusters_labels = utils.load(
op.join(BLENDER_ROOT_DIR, subject, 'fmri',
'clusters_labels_{}.npy'.format(contrast_name)))
if func_rois_folder == '':
func_rois_folder = op.join(SUBJECTS_DIR, subject, 'mmvt', 'fmri',
'functional_rois',
'{}_labels'.format(contrast_name))
utils.delete_folder_files(func_rois_folder)
for cl in clusters_labels:
cl_name = 'fmri_{}_{:.2f}'.format(cl['name'], cl['max'])
new_label = mne.Label(cl['vertices'],
cl['coordinates'],
hemi=cl['hemi'],
name=cl_name,
filename=None,
subject=subject,
verbose=None)
new_label.save(op.join(func_rois_folder, cl_name))
def save_labels_from_vertices_lookup(subject,
atlas,
subjects_dir,
surf_type='pial',
read_labels_from_fol=''):
# todo: Doens't work on DC, laus250. check that out
lookup = create_vertices_labels_lookup(
subject, atlas, read_labels_from_fol=read_labels_from_fol)
labels_fol = op.join(subjects_dir, subject, 'label', atlas)
utils.delete_folder_files(labels_fol)
for hemi in utils.HEMIS:
labels_vertices = defaultdict(list)
surf_fname = op.join(subjects_dir, subject, 'surf',
'{}.{}'.format(hemi, surf_type))
surf, _ = mne.surface.read_surface(surf_fname)
for vertice, label in lookup[hemi].items():
labels_vertices[label].append(vertice)
for label, vertices in labels_vertices.items():
new_label = mne.Label(sorted(vertices),
surf[vertices],
hemi=hemi,
name=label,
subject=subject)
new_label.save(op.join(labels_fol, label))
def subcortical_segmentation(subject, overwrite_subcortical_objs=False):
# Must source freesurfer. You need to have write permissions on SUBJECTS_DIR
if not op.isfile(op.join(SUBJECTS_DIR, subject, 'mri', 'norm.mgz')):
return False
script_fname = op.join(BRAINDER_SCRIPTS_DIR, 'aseg2srf')
if not op.isfile(script_fname):
raise Exception('The subcortical segmentation script is missing! {}'.format(script_fname))
if not utils.is_exe(script_fname):
utils.set_exe_permissions(script_fname)
# aseg2srf: For every subcortical region (8 10 11 12 13 16 17 18 26 47 49 50 51 52 53 54 58):
# 1) mri_pretess: Changes region segmentation so that the neighbors of all voxels have a face in common
# 2) mri_tessellate: Creates surface by tessellating
# 3) mris_smooth: Smooth the new surface
# 4) mris_convert: Convert the new surface into srf format
function_output_fol = op.join(SUBJECTS_DIR, subject, 'mmvt', 'subcortical_objs')
renamed_output_fol = op.join(SUBJECTS_DIR, subject, 'mmvt', 'subcortical')
lookup = load_subcortical_lookup_table()
obj_files = glob.glob(op.join(function_output_fol, '*.srf'))
if len(obj_files) < len(lookup) or overwrite_subcortical_objs:
utils.delete_folder_files(function_output_fol)
# utils.delete_folder_files(aseg_to_srf_output_fol)
utils.delete_folder_files(renamed_output_fol)
print('Trying to write into {}'.format(function_output_fol))
utils.run_script(ASEG_TO_SRF.format(subject))
# os.rename(aseg_to_srf_output_fol, function_output_fol)
ply_files = glob.glob(op.join(renamed_output_fol, '*.ply'))
if len(ply_files) < len(lookup) or overwrite_subcortical_objs:
convert_and_rename_subcortical_files(subject, function_output_fol, renamed_output_fol, lookup)
blender_dir = op.join(MMVT_DIR, subject, 'subcortical')
if not op.isdir(blender_dir) or len(glob.glob(op.join(blender_dir, '*.ply'))) < len(ply_files):
copy_subcorticals_to_blender(renamed_output_fol, subject)
flag_ok = len(glob.glob(op.join(blender_dir, '*.ply'))) == len(lookup) and \
len(glob.glob(op.join(blender_dir, '*.npz'))) == len(lookup)
return flag_ok
def calc_cbf_histograms(subject,
scan_rescan,
low_threshold,
high_threshold,
cortex_frac_threshold=0.9,
overwrite=False,
do_plot=True):
subject_fol = op.join(HOME_FOL, site, subject, scan_rescan)
output_fol = utils.make_dir(
op.join(op.join(RESULTS_FOL, 'aparc_aseg_hists', subject,
scan_rescan)))
values_output_fname = op.join(
op.join(RESULTS_FOL, 'aparc_aseg_hists', subject, scan_rescan,
'aparc_aseg_hist.pkl'))
means_output_fname = op.join(
op.join(RESULTS_FOL, 'aparc_aseg_hists', subject, scan_rescan,
'aparc_values.pkl'))
if op.isfile(values_output_fname) and op.isfile(
means_output_fname) and not overwrite and not do_plot:
return True
cics_cbf_fname = op.join(HOME_FOL, site, subject, scan_rescan, 'CBF.nii')
if not op.isfile(cics_cbf_fname):
print('calc_cbf_histograms: Cannot find {}!'.format(cics_cbf_fname))
return False
aparc_aseg_fname = op.join(subject_fol, 'aparc+aseg_cbf.mgz')
if not op.isfile(aparc_aseg_fname):
print('calc_cbf_histograms: Cannot find {}!'.format(aparc_aseg_fname))
return False
cortex_frac_fname = op.join(HOME_FOL, site, subject, scan_rescan,
'CBF.cortex.mgz')
if not op.isfile(cortex_frac_fname):
print('No cortex frac!')
return False
cbf_data = nib.load(cics_cbf_fname).get_data()
cortex_frac = nib.load(cortex_frac_fname).get_data()
lut = utils.read_freesurfer_lookup_table(return_dict=True)
aparc_aseg = nib.load(aparc_aseg_fname).get_data()
unique_codes = list(range(1001, 1036)) + list(range(2001, 2036))
if overwrite and do_plot:
utils.delete_folder_files(output_fol)
regions_values, regions_means = {}, {}
output_str = ''
for code in tqdm(unique_codes):
region_name = lut.get(code, None)
if region_name is None:
# print('{} not in lut!'.format(code))
continue
fig_fname = op.join(output_fol, '{}.jpg'.format(region_name))
if op.isfile(fig_fname) and not overwrite:
continue
region_values = cbf_data[np.where(aparc_aseg == code)]
cortex_frac_values = cortex_frac[np.where(aparc_aseg == code)]
cortex_indices = np.where(cortex_frac_values > cortex_frac_threshold)
if len(cortex_indices[0]) == 0:
output_str += '{} has no voxels with cortex_frac > {}!\n'.format(
region_name, cortex_frac_threshold)
continue
region_values = region_values[cortex_indices]
# regions_values[region_name] = region_values.copy()
in_bounderies_indices = np.where((low_threshold < region_values)
& (region_values < high_threshold))
region_values = region_values[in_bounderies_indices]
regions_values[region_name] = region_values.copy()
regions_means[region_name] = np.mean(regions_values[region_name])
# if len(outliers) > 0:
# output_str += '{} has {} out of {} values < {}\n'.format(
# region_name, len(outliers), len(region_values), low_threshold)
# outliers = np.where(region_values > high_threshold)[0]
# if len(outliers) > 0:
# output_str += '{} has {} out of {} values > {}\n'.format(
# region_name, len(outliers), len(region_values), high_threshold)
# region_values[region_values < low_threshold] = low_threshold
# region_values[region_values > high_threshold] = high_threshold
if do_plot:
plt.hist(region_values, bins=40)
plt.savefig(fig_fname)
plt.close()
print(output_str)
utils.save(regions_values, values_output_fname)
utils.save(regions_means, means_output_fname)
def language(args):
# -f language -s nmr01361 --clinical_dir clin_4090354
# -s nmr01353 -f clean_4d_data --fsd sycabs --remote_fmri_dir "/space/megraid/clinical/MEG-MRI/seder/freesurfer" --nconditions 4
if args.clinical_dir == '':
print('You should set the clinical_dir first. Example: clin_4090354')
return
clinical_root_dir = op.join(args.remote_fmri_dir, args.clinical_dir)
if not op.isdir(clinical_root_dir):
print('{} does not exist!'.format(clinical_root_dir))
task = 'sycabs'
fwhm = 6
subject = args.subject[0]
remote_mri_dir = args.remote_clinical_subjects_dir
subject_mri_dir = op.join(remote_mri_dir, subject)
mri_subject_task_dir = utils.make_dir(op.join(subject_mri_dir, task))
clinical_dirs = glob.glob(op.join(clinical_root_dir, '*'))
clinical_dirs = [
d for d in clinical_dirs if utils.namebase(d) != 'mne_dcm'
]
remote_fmri_dir = utils.select_one_file(clinical_dirs)
fmri_fols = sorted(glob.glob(op.join(remote_fmri_dir, '*_SyCAbs')))
par_fol = utils.make_dir(op.join(remote_mri_dir, subject, 'par'))
par_files = glob.glob(op.join(par_fol, '*.par'))
sessions = sorted(
[utils.find_num_in_str(utils.namebase(d))[0] for d in fmri_fols])
# Warning: You first need to put the original ones in the following folder:
if len(par_files) == 0:
print('\n *** Please put the original par files in {} and rerun ***'.
format(op.join(remote_mri_dir, subject, 'par')))
return
par_files.sort(key=lambda x: int(utils.namebase(x).split('_')[-1]))
ret = input('''
Patient: {}
MRI folder: {}
fMRI root folder: {}
fMRI sessions: {}
Session and pars: {}
Do you want to continue (y/n)? '''.format(
subject, subject_mri_dir, remote_fmri_dir,
[utils.namebase(d) for d in fmri_fols],
list(zip([utils.namebase(f) for f in par_files], sessions))))
if not au.is_true(ret):
return
# You need first to run src.preproc.anatomy
if not op.isfile(anat.get_blend_fname(subject, args.atlas)):
args = anat.read_cmd_args(
dict(
subject=subject,
remote_subject_dir=subject_mri_dir,
ignore_missing=True,
))
pu.run_on_subjects(args, anat.main)
# convert the fMRI dicom files to nii
for fmri_fol in fmri_fols:
ses_num = utils.find_num_in_str(utils.namebase(fmri_fol))[0]
ses_files = glob.glob(op.join(fmri_fol, '**', '*.*'), recursive=True)
output_fname = op.join(
utils.make_dir(op.join(mri_subject_task_dir, ses_num)), 'f.nii.gz')
if not op.isfile(output_fname):
fu.mri_convert(ses_files[0], output_fname)
# Convert and arrange the par file
from src.misc.fmri_scripts import convert_par
for par_file, session in zip(par_files, sessions):
fs_par_fname = op.join(mri_subject_task_dir, session,
'{}.par'.format(task))
# if not op.isfile(fs_par_fname):
warnings = convert_par.sycabs(par_file, fs_par_fname)
if warnings != '':
print(
'\n *** Please fix the problems with the par convertion ({}) and rerun ***\n'
.format(par_file))
return
for hemi in utils.HEMIS:
utils.delete_folder_files(
op.join(remote_mri_dir, '{}_sm{}_{}'.format(task, fwhm, hemi)))
# Run the FreeSurfer analysis
args = fmri.read_cmd_args(
dict(subject=subject,
atlas=args.atlas,
function='clean_4d_data',
fsd=task,
fwhm=fwhm,
remote_fmri_dir=remote_mri_dir,
nconditions=4,
ignore_missing=True,
print_only=False,
overwrite_4d_preproc=False))
pu.run_on_subjects(args, fmri.main)
# Load the fMRI results
args = fmri.read_cmd_args(
dict(
subject=subject,
atlas=args.atlas,
function='load_surf_files',
fmri_file_template=op.join(MMVT_DIR, subject, 'fmri',
'words_v_symbols_{hemi}.mgz'),
))
pu.run_on_subjects(args, fmri.main)
def calc_cortical_histograms(subject,
scan_rescan,
atlas,
low_threshold=40,
high_threshold=100,
overwrite=False,
do_plot=True,
n_jobs=4):
if not lu.check_labels(subject, atlas, SUBJECTS_DIR, MMVT_DIR):
return False
output_fol = utils.make_dir(
op.join(MMVT_DIR, subject, 'ASL', scan_rescan,
'labels_hists_{}'.format(atlas)))
output_fname = op.join(MMVT_DIR, subject, 'ASL', scan_rescan,
'labels_hists_{}.pkl'.format(atlas))
if overwrite:
utils.delete_folder_files(output_fol)
print('Saving figures into {}'.format(output_fol))
labels_data = {}
for hemi in utils.HEMIS:
npy_data_fname = op.join(
MMVT_DIR, subject, 'fmri',
'fmri_CBF_{}_{}.npy'.format(scan_rescan, hemi))
if not op.isfile(npy_data_fname):
print('Cannot find hemi data file! ({})'.format(npy_data_fname))
return False
surf_fname = op.join(SUBJECTS_DIR, subject, 'surf',
'{}.pial'.format(hemi))
if not op.isfile(surf_fname):
print('Cannot find surface file! ({})'.format(surf_fname))
return False
hemi_vals = np.load(npy_data_fname)
labels = lu.read_labels(subject,
SUBJECTS_DIR,
atlas,
hemi=hemi,
n_jobs=n_jobs)
labels_vertives_num = max([max(l.vertices) for l in labels])
hemi_data_vertices_num = len(hemi_vals) - 1
if labels_vertives_num != hemi_data_vertices_num:
print(
'Wrong number of vertices or labels! labels_vertives_num ({}) != len({})'
.format(labels_vertives_num, len(hemi_vals)))
return False
for label in tqdm(labels):
fig_fname = op.join(output_fol, '{}.jpg'.format(label.name))
if op.isfile(fig_fname) and not overwrite:
continue
labels_data[label.name] = label_data = hemi_vals[label.vertices]
outliers = np.where(label_data < low_threshold)[0]
if len(outliers) > 0:
print('{} has {}/{} values < {}'.format(
label.name, len(outliers), len(label_data), low_threshold))
outliers = np.where(label_data > high_threshold)[0]
if len(outliers) > 0:
print('{} has {}/{} values > {}'.format(
label.name, len(outliers), len(label_data),
high_threshold))
label_data[label_data < low_threshold] = low_threshold
label_data[label_data > high_threshold] = high_threshold
if do_plot:
plt.hist(label_data, bins=40)
plt.savefig(fig_fname)
plt.close()
utils.save(labels_data, output_fname)