def calc_labels_avg(target_subject, hemi, atlas, fmri_fname, res_dir, cwd, overwrite=True, output_txt_fname='',
output_sum_fname='', ret_files_name=False, **kargs):
def get_labels_names(line):
label_name = line.split()[4]
label_nums = utils.find_num_in_str(label_name)
label_num = label_nums[-1] if len(label_nums) > 0 else ''
if label_num != '':
name_len = label_name.find('_{}'.format(label_num)) + len(str(label_num)) + 1
label_name = '{}-{}'.format(label_name[:name_len], hemi)
return label_name
if output_txt_fname == '':
output_txt_fname = op.join(res_dir, '{}_{}_{}.txt'.format(utils.namebase(fmri_fname), atlas, hemi))
if output_sum_fname == '':
output_sum_fname = op.join(res_dir, '{}_{}_{}.sum'.format(utils.namebase(fmri_fname), atlas, hemi))
if not op.isfile(output_txt_fname) or not op.isfile(output_sum_fname) or overwrite:
print('Running mri_segstats on {} ({})'.format(fmri_fname, utils.file_modification_time(fmri_fname)))
utils.partial_run_script(locals(), cwd=cwd)(mri_segstats)
if not op.isfile(output_txt_fname):
raise Exception('The output file was not created!')
labels_data = np.genfromtxt(output_txt_fname).T
labels_names = utils.read_list_from_file(output_sum_fname, get_labels_names, 'rb')
if ret_files_name:
return labels_data, labels_names, output_txt_fname, output_sum_fname
else:
return labels_data, labels_names
def _morph_electrodes_parallel(p):
subjects, subject_to, subjects_dir, mmvt_dir, output_fname, overwrite, print_only = p
bad_subjects, good_subjects = [], []
for subject_from in subjects:
electrodes_to_morph_file_name = 'electrodes_to_morph'
morphed_electrodes_file_name = 'electrodes_morph_to_{}'.format(
subject_to)
output_fname = op.join(mmvt_dir, subject_from, 'electrodes',
'{}.txt'.format(morphed_electrodes_file_name))
if op.isfile(output_fname) and not overwrite:
print('{} electrode were already morphed to {}'.format(
subject_from, subject_to))
continue
if subject_to == 'fsaverage':
subject_to = 'cvs_avg35_inMNI152'
rs = utils.partial_run_script(locals(), print_only=print_only)
if subject_to == 'cvs_avg35_inMNI152':
rs(apply_morph_mni)
else:
rs(apply_morph)
if op.isfile(output_fname):
print('{}: electrodes file was morphed successfuly! -> {}'.format(
subject_from, output_fname))
else:
print('{}: Couldn\'t morph the electrodes file!'.format(
subject_from))
def warp_buckner_atlas(subject,
subjects_dir,
bunker_atlas_fname,
wrap_map_fname,
print_only=False,
**kargs):
norm_fname = op.join(subjects_dir, subject, 'mri', 'norm.mgz')
if not op.isfile(norm_fname):
print("Error in warp_buckner_atlas, can't find the file {}".format(
norm_fname))
return False
trans_fname = op.join(subjects_dir, subject, 'mri', 'transforms',
'talairach.m3z')
if not op.isfile(trans_fname):
print("Error in warp_buckner_atlas, can't find the file {}".format(
trans_fname))
return False
wrap_map_name = op.basename(wrap_map_fname)
# todo: check why we need to chage directory here
current_dir = os.getcwd()
os.chdir(op.join(subjects_dir, subject, 'mri'))
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(warp_buckner_atlas_cmd)
os.chdir(current_dir)
if not op.isfile(wrap_map_fname):
raise Exception('Error in warp_buckner_atlas!')
else:
print('warp_buckner_atlas output fname: {}'.format(wrap_map_fname))
return True
def create_annotation_file(subject, atlas, subjects_dir='', freesurfer_home='', overwrite_annot_file=True, print_only=False):
'''
Creates the annot file by using the freesurfer mris_ca_label function
Parameters
----------
subject: subject name
atlas: One of the three atlases included with freesurfer:
Possible values are aparc.DKTatlas40, aparc.a2009s or aparc
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
subjects_dir: subjects dir. If empty, get it from the environ
freesurfer_home: freesurfer home. If empty, get it from the environ
overwrite_annot_file: If False and the annot file already exist, the function return True. If True, the function
delete first the annot files if exist.
print_only: If True, the function will just prints the command without executing it
Returns
-------
True if the new annot files exist
'''
atlas_types = {'aparc': 'curvature.buckner40.filled.desikan_killiany',
'aparc.a2009s': 'destrieux.simple.2009-07-28',
'aparc.DKTatlas40': 'DKTatlas40'}
atlas_type = atlas_types[atlas]
check_env_var('FREESURFER_HOME', freesurfer_home)
check_env_var('SUBJECTS_DIR', subjects_dir)
annot_files_exist = True
for hemi in ['rh','lh']:
annot_fname = op.join(subjects_dir, subject, 'label', '{}.{}.annot'.format(hemi, atlas))
if overwrite_annot_file and op.isfile(annot_fname):
os.remove(annot_fname)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mris_ca_label)
annot_files_exist = annot_files_exist and op.isfile(annot_fname)
return annot_files_exist
def aseg_to_srf(subject, subjects_dir, output_fol, region_id, mask_fname, norm_fname,
overwrite_subcortical_objs=False):
ret = True
tmp_fol = op.join(subjects_dir, subject, 'tmp', utils.rand_letters(6))
utils.make_dir(tmp_fol)
rs = utils.partial_run_script(locals())
output_fname = op.join(output_fol, '{}.srf'.format(region_id))
tmp_output_fname = op.join(tmp_fol, '{}.asc'.format(region_id))
if overwrite_subcortical_objs:
utils.remove_file(output_fname)
try:
rs(mri_pretess)
rs(mri_tessellate)
rs(mris_smooth)
rs(mris_convert)
if op.isfile(tmp_output_fname):
shutil.move(tmp_output_fname, output_fname)
shutil.rmtree(tmp_fol)
else:
ret = False
except:
print('Error in aseg_to_srf! subject: {}'.format(subject))
print(traceback.format_exc())
ret = False
return ret
def create_seghead(subject, subjects_dir=None, print_only=False, **kargs):
if subjects_dir is None:
subjects_dir = utils.get_link_dir(utils.get_links_dir(), 'subjects',
'SUBJECTS_DIR')
os.environ['SUBJECTS_DIR'] = subjects_dir
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mkheadsurf)
def check_cbf_to_t1_registeration(subject,
site,
scan_rescan,
print_only=False):
subject_fol = op.join(HOME_FOL, site, subject, scan_rescan)
subject_fs_fol = op.join(FS_ROOT,
get_subject_fs_folder(subject, scan_rescan))
orig_fname = op.join(subject_fs_fol, 'mri', 'orig.mgz')
control_fname = op.join(subject_fol, 'Control.nii')
lta_fname = op.join(subject_fol, 'control_to_T1.lta')
lh_white = op.join(subject_fs_fol, 'surf', 'lh.white')
rh_white = op.join(subject_fs_fol, 'surf', 'rh.white')
cmd = 'freeview -transform-volume -viewport cor -v "{orig_fname}":visible=0:name=orig.mgz ' + \
'"{control_fname}":name=Control.nii:reg="{lta_fname}" --surface ' + \
'"{lh_white}":edgecolor=yellow --surface "{rh_white}":edgecolor=yellow'
utils.partial_run_script(locals(), print_only=print_only)(cmd)
def combine_images(fol, movie_name, frame_rate=10, start_number=-1, images_prefix='', images_format='',
images_type='', ffmpeg_cmd='ffmpeg', movie_name_full_path=False, debug=False,
copy_files=False, **kwargs):
images_type, images_prefix, images_format, images_format_len, start_number = find_images_props(
fol, start_number, images_prefix, images_format, images_type)
if movie_name == '' and images_prefix != '':
movie_name = images_prefix
elif movie_name == '':
movie_name = 'output_video'
org_fol = fol
if utils.is_windows() or copy_files:
fol = change_frames_names(fol, images_prefix, images_type, images_format_len)
images_prefix = op.join(fol, images_prefix)
if not movie_name_full_path:
movie_name = op.join(fol, movie_name)
combine_images_cmd = '{ffmpeg_cmd} -framerate {frame_rate} '
if start_number != 1:
# You might want to use a static ffmpeg if your ffmepg version doesn't support the start_number flag, like:
# ffmpeg_cmd = '~/space1/Downloads/ffmpeg-git-static/ffmpeg'
combine_images_cmd += '-start_number {start_number} '
# Not working in windows:
# combine_images_cmd += '-pattern_type glob -i "*.{images_type}" '
combine_images_cmd += '-i {images_prefix}{images_format}.{images_type} '
# http://stackoverflow.com/questions/20847674/ffmpeg-libx264-height-not-divisible-by-2
combine_images_cmd += '-vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" '
combine_images_cmd += '-c:v libx264 -r 30 -pix_fmt yuv420p {movie_name}.mp4'
if debug:
combine_images_cmd += ' -loglevel debug'
rs = utils.partial_run_script(locals())
rs(combine_images_cmd)
with open(op.join(org_fol, 'combine_images_cmd.txt'), 'w') as f:
f.write(combine_images_cmd.format(**locals()))
return '{}.mp4'.format(movie_name)
def combine_images(fol, movie_name, frame_rate=10, start_number=-1, images_prefix='', images_format='',
images_type='', ffmpeg_cmd='ffmpeg', **kwargs):
if images_type == '':
images_types = set([utils.file_type(image) for image in glob.glob(op.join(fol, '{}*.*'.format(images_prefix)))])
for opt_type in ['png', 'jpg', 'bmp', 'gif']:
if opt_type in images_types:
images_type = opt_type
print('Images type is {}'.format(images_type))
break
if images_type == '':
raise Exception("Can't find the images type!")
images = glob.glob(op.join(fol, '{}*.{}'.format(images_prefix, images_type)))
image_nb = utils.namebase(images[0])
number = utils.read_numbers_rx(image_nb)[0]
if images_prefix == '':
images_prefix = image_nb[:-len(number)]
if images_format == '':
images_format = '%0{}d'.format(len(number))
if start_number == -1:
start_number = min([int(utils.namebase(image)[len(images_prefix):]) for image in images])
images_prefix = op.join(fol, images_prefix)
movie_name = op.join(fol, movie_name)
combine_images_cmd = '{ffmpeg_cmd} -framerate {frame_rate} '
if start_number > 1:
# You might want to use a static ffmpeg if your ffmepg version doesn't support the start_number flag, like:
# ffmpeg_cmd = '~/space1/Downloads/ffmpeg-git-static/ffmpeg'
combine_images_cmd += '-start_number {start_number} '
combine_images_cmd += '-i {images_prefix}{images_format}.{images_type} '
# http://stackoverflow.com/questions/20847674/ffmpeg-libx264-height-not-divisible-by-2
combine_images_cmd += '-vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" '
combine_images_cmd += '-c:v libx264 -r 30 -pix_fmt yuv420p {movie_name}.mp4'
rs = utils.partial_run_script(locals())
rs(combine_images_cmd)
def create_aparc_aseg_file(subject,
atlas,
subjects_dir,
overwrite_aseg_file=False,
print_only=False,
**kargs):
if not utils.both_hemi_files_exist(
op.join(subjects_dir, subject, 'label', '{}.{}.annot'.format(
'{hemi}', atlas))):
print('No annot file was found for {}!'.format(atlas))
return False, ''
# The atlas var need to be in the locals for the APARC2ASEG call
aparc_aseg_file = '{}+aseg.mgz'.format(atlas)
mri_file_fol = op.join(subjects_dir, subject, 'label')
aparc_aseg_fname = op.join(mri_file_fol, aparc_aseg_file)
rs = utils.partial_run_script(locals(),
print_only=print_only,
cwd=mri_file_fol)
if not op.isfile(aparc_aseg_fname) or overwrite_aseg_file:
now = time.time()
rs(mri_aparc2aseg)
if op.isfile(aparc_aseg_fname) and op.getmtime(aparc_aseg_fname) > now:
return True, aparc_aseg_fname
else:
print('Failed to create {}'.format(aparc_aseg_fname))
return False, ''
return True, aparc_aseg_fname
def flat_brain(subject, hemi, subjects_dir, print_only=False):
# mris_flatten lh.inflated.patch lh.flat.patch
surf_dir = op.join(subjects_dir, subject, 'surf')
rs = utils.partial_run_script(locals(),
cwd=surf_dir,
print_only=print_only)
rs(mris_flatten)
return op.join(surf_dir, '{}.flat.patch'.format(hemi))
def flat_brain(subject, hemi, subjects_dir, print_only=False, **kargs):
# mris_flatten lh.inflated.patch lh.flat.patch
surf_dir = op.join(subjects_dir, subject, 'surf')
rs = utils.partial_run_script(locals(),
cwd=surf_dir,
print_only=print_only)
rs(mris_flatten)
return get_flat_patch_fname(subject, hemi, subjects_dir)
def robust_register(subject, subjects_dir, source_fname, target_fname, output_fname, lta_name,
cost_function='nmi', print_only=False, **kargs):
xfms_dir = op.join(subjects_dir, subject, 'mri', 'transforms')
utils.make_dir(xfms_dir)
lta_fname = op.join(xfms_dir, lta_name)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mri_robust_register)
return True if print_only else op.isfile(lta_fname)
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 transform_mni_to_subject(subject,
subjects_dir,
mni305_sig_file,
subject_sig_file,
print_only=False,
**kargs):
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mni305_to_subject_reg)
rs(mni305_to_subject)
def mask_to_srf(atlas_fol, region, hemi, colin_norm_fname):
os.chdir(atlas_fol)
rs = utils.partial_run_script(locals())
# rs(MRI_PRETESS)
rs(MRI_TESSELLATE)
rs(MRIS_SMOOTH)
rs(MRIS_CONVERT)
shutil.move(op.join(atlas_fol, 'tmp', '{}_{}.asc'.format(region, hemi)),
op.join(atlas_fol, 'tmp', '{}_{}.srf'.format(region, hemi)))
def mask_to_srf(atlas_fol, region, hemi, colin_norm_fname):
os.chdir(atlas_fol)
rs = utils.partial_run_script(locals())
# rs(MRI_PRETESS)
rs(MRI_TESSELLATE)
rs(MRIS_SMOOTH)
rs(MRIS_CONVERT)
shutil.move(op.join(atlas_fol, 'tmp', '{}_{}.asc'.format(region, hemi)),
op.join(atlas_fol, 'tmp', '{}_{}.srf'.format(region, hemi)))
def project_pet_volume_data(subject, volume_fname, hemi, output_fname=None, projfrac=0.5, print_only=False):
temp_output = output_fname is None
if output_fname is None:
output_fname = mktemp(prefix="pysurfer-v2s", suffix='.mgz')
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mri_vol2surf_pet)
surf_data = read_scalar_data(output_fname)
if temp_output:
os.remove(output_fname)
return surf_data
def project_pet_volume_data(subject, volume_fname, hemi, output_fname=None, projfrac=0.5, print_only=False, **kargs):
temp_output = output_fname is None
if output_fname is None:
output_fname = mktemp(prefix="pysurfer-v2s", suffix='.mgz')
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mri_vol2surf_pet)
surf_data = read_scalar_data(output_fname)
if temp_output:
os.remove(output_fname)
return surf_data
def transform_mni_to_subject(subject, subjects_dir, volue_fol, volume_fname='sig.mgz',
subject_contrast_file_name='sig_subject.mgz', print_only=False):
mni305_sig_file = os.path.join(volue_fol, volume_fname)
subject_sig_file = os.path.join(volue_fol, subject_contrast_file_name)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mni305_to_subject_reg)
rs(mni305_to_subject)
subject_fol = op.join(subjects_dir, subject, 'mmvt')
utils.make_dir(subject_fol)
shutil.move(op.join(utils.get_parent_fol(), 'mn305_to_{}.dat'.format(subject)),
op.join(subject_fol, 'mn305_to_{}.dat'.format(subject)))
def vol2vol(subject,
source_volume_fname,
target_volume_fname,
output_volume_fname,
cwd=None,
print_only=False):
if source_volume_fname != target_volume_fname:
rs = utils.partial_run_script(locals(), cwd=cwd, print_only=print_only)
rs(mri_vol2vol)
if not op.isfile(output_volume_fname):
raise Exception('vol2vol: Target file was not created!')
def surf2surf(source_subject,
target_subject,
hemi,
source_fname,
target_fname,
cwd=None,
print_only=False):
if source_subject != target_subject:
rs = utils.partial_run_script(locals(), cwd=cwd, print_only=print_only)
rs(mri_surf2surf)
if not op.isfile(target_fname):
raise Exception('surf2surf: Target file was not created!')
def robust_register_to_template(subjects,
template_system,
subjects_dir,
vox2vox=False,
print_only=False):
subject_to = 'fsaverage5' if template_system == 'ras' else 'colin27' if template_system == 'mni' else template_system
for subject_from in subjects:
cmd = mri_robust_register
lta_name = 't1_to_{}'.format(subject_to)
if vox2vox:
cmd += ' --vox2vox'
lta_name += '_vox2vox'
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(cmd)
def transform_mni_to_subject(subject,
subjects_dir,
volue_fol,
volume_fname='sig.mgz',
subject_contrast_file_name='sig_subject.mgz',
print_only=False):
mni305_sig_file = os.path.join(volue_fol, volume_fname)
subject_sig_file = os.path.join(volue_fol, subject_contrast_file_name)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mni305_to_subject_reg)
rs(mni305_to_subject)
subject_fol = op.join(subjects_dir, subject, 'mmvt')
utils.make_dir(subject_fol)
shutil.move(
op.join(utils.get_parent_fol(), 'mn305_to_{}.dat'.format(subject)),
op.join(subject_fol, 'mn305_to_{}.dat'.format(subject)))
def aseg_to_srf(subject,
subjects_dir,
output_fol,
region_id,
lookup,
mask_fname,
norm_fname,
overwrite_subcortical_objs=False,
**kargs):
from src.utils import geometry_utils as gu
ret = True
tmp_fol = op.join(subjects_dir, subject, 'tmp', utils.rand_letters(6))
utils.make_dir(tmp_fol)
rs = utils.partial_run_script(locals())
# output_fname = op.join(output_fol, '{}.srf'.format(region_id))
# tmp_output_fname = op.join(tmp_fol, '{}.asc'.format(region_id))
# if overwrite_subcortical_objs:
# utils.remove_file(output_fname)
try:
rs(mri_pretess)
rs(mri_tessellate)
rs(mris_smooth)
fs_file = op.join(tmp_fol, '{}_smooth'.format(region_id))
verts, faces = gu.read_surface(fs_file)
# verts, faces = nib_fs.read_geometry(fs_file)
num = int(op.basename(fs_file).split('_')[0])
if num not in lookup:
print('Error in the subcorticals lookup table!')
return False
new_name = lookup.get(num, '')
utils.write_ply_file(verts, faces,
op.join(output_fol, '{}.ply'.format(new_name)),
True)
# mris_convert = 'mris_convert {tmp_fol}/{region_id}_smooth {tmp_fol}/{region_id}.asc'
# rs(mris_convert)
# if op.isfile(tmp_output_fname):
# shutil.move(tmp_output_fname, output_fname)
if op.isdir(tmp_fol):
shutil.rmtree(tmp_fol)
else:
ret = False
except:
print('Error in aseg_to_srf! subject: {}'.format(subject))
print(traceback.format_exc())
ret = False
return ret
def morph_t1(subjects, template_system, subjects_dir, print_only=False):
subject_to = 'fsaverage5' if template_system == 'ras' else 'colin27' if template_system == 'mni' else template_system
for subject in subjects:
if not op.isfile(
op.join(subjects_dir, subject, 'mri_cvs_register_to_colin27',
'final_CVSmorph_tocolin27.m3z')):
print(
f'The m3z morph matrix does not exist for subject {subject}!')
continue
output_fname = op.join(subjects_dir, subject, 'mri',
'T1_to_colin_csv_register.mgz')
if not op.isfile(output_fname):
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mri_vol2vol)
print(
f'freeview -v {subjects_dir}/colin27/mri/T1.mgz {subjects_dir}/{subject}/mri/T1_to_colin_csv_register.mgz'
)
def combine_images(fol,
movie_name,
frame_rate=10,
start_number=-1,
images_prefix='',
images_format='',
images_type='',
ffmpeg_cmd='ffmpeg',
**kwargs):
if images_type == '':
images_types = set([
utils.file_type(image)
for image in glob.glob(op.join(fol, '{}*.*'.format(images_prefix)))
])
for opt_type in ['png', 'jpg', 'bmp', 'gif']:
if opt_type in images_types:
images_type = opt_type
print('Images type is {}'.format(images_type))
break
if images_type == '':
raise Exception("Can't find the images type!")
images = glob.glob(
op.join(fol, '{}*.{}'.format(images_prefix, images_type)))
image_nb = utils.namebase(images[0])
number = utils.read_numbers_rx(image_nb)[0]
if images_prefix == '':
images_prefix = image_nb[:-len(number)]
if images_format == '':
images_format = '%0{}d'.format(len(number))
if start_number == -1:
start_number = min([
int(utils.namebase(image)[len(images_prefix):]) for image in images
])
images_prefix = op.join(fol, images_prefix)
movie_name = op.join(fol, movie_name)
combine_images_cmd = '{ffmpeg_cmd} -framerate {frame_rate} '
if start_number > 1:
# You might want to use a static ffmpeg if your ffmepg version doesn't support the start_number flag, like:
# ffmpeg_cmd = '~/space1/Downloads/ffmpeg-git-static/ffmpeg'
combine_images_cmd += '-start_number {start_number} '
combine_images_cmd += '-i {images_prefix}{images_format}.{images_type} '
# http://stackoverflow.com/questions/20847674/ffmpeg-libx264-height-not-divisible-by-2
combine_images_cmd += '-vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" '
combine_images_cmd += '-c:v libx264 -r 30 -pix_fmt yuv420p {movie_name}.mp4'
rs = utils.partial_run_script(locals())
rs(combine_images_cmd)
def warp_buckner_atlas(subject, subjects_dir, bunker_atlas_fname, wrap_map_fname, print_only=False):
norm_fname = op.join(subjects_dir, subject, 'mri', 'norm.mgz')
if not op.isfile(norm_fname):
print("Error in warp_buckner_atlas, can't find the file {}".format(norm_fname))
return False
trans_fname = op.join(subjects_dir, subject, 'mri', 'transforms', 'talairach.m3z')
if not op.isfile(trans_fname):
print("Error in warp_buckner_atlas, can't find the file {}".format(trans_fname))
return False
wrap_map_name = op.basename(wrap_map_fname)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(warp_buckner_atlas_cmd)
if not op.isfile(wrap_map_fname):
raise Exception('Error in warp_buckner_atlas!')
else:
print('warp_buckner_atlas output fname: {}'.format(wrap_map_fname))
return True
def create_annotation_file(subject,
atlas,
subjects_dir='',
freesurfer_home='',
overwrite_annot_file=True,
print_only=False,
**kargs):
'''
Creates the annot file by using the freesurfer mris_ca_label function
Parameters
----------
subject: subject name
atlas: One of the three atlases included with freesurfer:
Possible values are aparc.DKTatlas, aparc.a2009s or aparc
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
subjects_dir: subjects dir. If empty, get it from the environ
freesurfer_home: freesurfer home. If empty, get it from the environ
overwrite_annot_file: If False and the annot file already exist, the function return True. If True, the function
delete first the annot files if exist.
print_only: If True, the function will just prints the command without executing it
Returns
-------
True if the new annot files exist
'''
atlas_types = {
'aparc': 'curvature.buckner40.filled.desikan_killiany',
'aparc.a2009s': 'destrieux.simple.2009-07-28',
'aparc.DKTatlas': 'DKTatlas',
'aparc.DKTatlas40': 'DKTatlas40'
}
atlas_type = atlas_types[atlas]
check_env_var('FREESURFER_HOME', freesurfer_home)
check_env_var('SUBJECTS_DIR', subjects_dir)
annot_files_exist = True
for hemi in ['rh', 'lh']:
annot_fname = op.join(subjects_dir, subject, 'label',
'{}.{}.annot'.format(hemi, atlas))
if overwrite_annot_file and op.isfile(annot_fname):
os.remove(annot_fname)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(mris_ca_label)
annot_files_exist = annot_files_exist and op.isfile(annot_fname)
return annot_files_exist
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 _morph_electrodes_parallel(p):
subjects, subject_to, subjects_dir, overwrite, print_only = p
bad_subjects, good_subjects = [], []
for subject_from in subjects:
output_fname = op.join(subjects_dir, subject_from, 'electrodes',
f'stim_electrodes_to_{subject_to}.txt')
if op.isfile(output_fname) and not overwrite:
continue
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(applyMorph)
ret = op.isfile(output_fname)
if not ret:
bad_subjects.append(subject_from)
else:
good_subjects.append(subject_from)
print('good subjects: {}'.format(good_subjects))
print('bad subjects: {}'.format(bad_subjects))
def calc_volume_fractions(subject,
subject_fol,
scan_rescan,
overwrite=False,
print_only=False,
check_if_should_run=False,
verbose=True):
reg_fname = op.join(subject_fol, 'control_to_T1.lta')
output_fname = op.join(subject_fol, 'CBF')
output_mgz_fname = op.join(subject_fol, 'CBF.cortex.mgz')
do_run, ret = cics_checks([reg_fname], [output_fname], subject_fol,
check_if_should_run, overwrite, verbose)
if not do_run:
return ret
set_subject(subject, scan_rescan)
rs = utils.partial_run_script(locals(), print_only=print_only)
# mri_compute_volume_fractions_reg = 'mri_compute_volume_fractions --o "{output_fname}" --reg "{reg_fname}"'
rs(mri_compute_volume_fractions_reg)
return output_exists()
def create_aparc_aseg_file(subject, args): #atlas, print_only=False, overwrite=False, check_mgz_values=False):
necessary_files = {'surf': ['lh.white', 'rh.white'], 'mri': ['ribbon.mgz']}
utils.check_for_necessary_files(necessary_files, op.join(SUBJECTS_DIR, subject))
# The atlas var need to be in the locals for the APARC2ASEG call
atlas = args.atlas
rs = utils.partial_run_script(locals(), print_only=False)
aparc_aseg_file = '{}+aseg.mgz'.format(args.atlas)
mri_file_fol = op.join(SUBJECTS_DIR, subject, 'mri')
mri_file = op.join(mri_file_fol, aparc_aseg_file)
blender_file = op.join(MMVT_DIR, subject, 'freeview', aparc_aseg_file)
if not op.isfile(blender_file) or args.overwrite_aseg_file:
current_dir = op.dirname(op.realpath(__file__))
os.chdir(mri_file_fol)
now = time.time()
rs(APARC2ASEG)
if op.isfile(mri_file) and op.getmtime(mri_file) > now:
shutil.copyfile(mri_file, blender_file)
else:
print('Failed to create {}'.format(mri_file))
os.chdir(current_dir)
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 register_aseg_to_cbf(subject,
subject_fol,
scan_rescan,
overwrite=False,
print_only=True,
check_if_should_run=False,
verbose=True):
lta_fname = op.join(subject_fol, 'control_to_T1.lta')
source_fname = op.join(FS_ROOT,
get_subject_fs_folder(subject, scan_rescan), 'mri',
'aparc+aseg.mgz')
output_fname = op.join(subject_fol, 'aparc+aseg_cbf.mgz')
do_run, ret = cics_checks([lta_fname, source_fname], [output_fname],
subject_fol, check_if_should_run, overwrite,
verbose)
if not do_run:
return ret
subject = set_subject(subject, scan_rescan)
rs = utils.partial_run_script(locals(), print_only=print_only)
# 'mri_convert -ait "{lta_fname}" "{source_fname}" "{output_fname}"'
rs(register_using_inverse_lta)
return op.isfile(output_fname)
def register_cbf_to_t1(subject,
subject_fol,
scan_rescan,
overwrite=False,
print_only=False,
check_if_should_run=False,
verbose=True):
output_fname = op.join(subject_fol, 'Control_to_T1.nii')
lta_fname = op.join(subject_fol, 'control_to_T1.lta')
source_fname = op.join(subject_fol, 'Control.nii')
target_fname = op.join(FS_ROOT,
get_subject_fs_folder(subject,
scan_rescan), 'mri', 'T1.mgz')
do_run, ret = cics_checks([source_fname, target_fname],
[output_fname, lta_fname], subject_fol,
check_if_should_run, overwrite, verbose)
if not do_run:
return ret
set_subject(subject, scan_rescan)
rs = utils.partial_run_script(locals(), print_only=print_only)
# bbregister --s {subject} --mov "{source_fname}" --lta "{lta_fname}" --t1 --o "{output_fname}"
rs(bbregister)
return all([op.isfile(fname) for fname in [output_fname, lta_fname]])
def create_aparc_aseg_file(
subject, args
): #atlas, print_only=False, overwrite=False, check_mgz_values=False):
necessary_files = {'surf': ['lh.white', 'rh.white'], 'mri': ['ribbon.mgz']}
utils.check_for_necessary_files(necessary_files,
op.join(SUBJECTS_DIR, subject))
# The atlas var need to be in the locals for the APARC2ASEG call
atlas = args.atlas
rs = utils.partial_run_script(locals(), print_only=False)
aparc_aseg_file = '{}+aseg.mgz'.format(args.atlas)
mri_file_fol = op.join(SUBJECTS_DIR, subject, 'mri')
mri_file = op.join(mri_file_fol, aparc_aseg_file)
blender_file = op.join(BLENDER_ROOT_DIR, subject, 'freeview',
aparc_aseg_file)
if not op.isfile(blender_file) or args.overwrite_aseg_file:
current_dir = op.dirname(op.realpath(__file__))
os.chdir(mri_file_fol)
now = time.time()
rs(APARC2ASEG)
if op.isfile(mri_file) and op.getmtime(mri_file) > now:
shutil.copyfile(mri_file, blender_file)
else:
print('Failed to create {}'.format(mri_file))
os.chdir(current_dir)
def warp_buckner_atlas(subject,
subjects_dir,
bunker_atlas_fname,
wrap_map_fname,
print_only=False):
norm_fname = op.join(subjects_dir, subject, 'mri', 'norm.mgz')
if not op.isfile(norm_fname):
print("Error in warp_buckner_atlas, can't find the file {}".format(
norm_fname))
return False
trans_fname = op.join(subjects_dir, subject, 'mri', 'transforms',
'talairach.m3z')
if not op.isfile(trans_fname):
print("Error in warp_buckner_atlas, can't find the file {}".format(
trans_fname))
return False
wrap_map_name = op.basename(wrap_map_fname)
rs = utils.partial_run_script(locals(), print_only=print_only)
rs(warp_buckner_atlas_cmd)
if not op.isfile(wrap_map_fname):
raise Exception('Error in warp_buckner_atlas!')
else:
print('warp_buckner_atlas output fname: {}'.format(wrap_map_fname))
return True
