def freesurfer_surface_to_blender_surface(subject, hemi='both', overwrite=False):
for hemi in utils.get_hemis(hemi):
utils.make_dir(op.join(MMVT_DIR, subject, 'surf'))
for surf_type in ['inflated', 'pial']:
surf_name = op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}'.format(hemi, surf_type))
surf_wavefront_name = '{}.asc'.format(surf_name)
surf_new_name = '{}.srf'.format(surf_name)
hemi_ply_fname = '{}.ply'.format(surf_name)
mmvt_hemi_ply_fname = op.join(MMVT_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type))
mmvt_hemi_npz_fname = op.join(MMVT_DIR, subject, 'surf', '{}.{}.npz'.format(hemi, surf_type))
if overwrite or not op.isfile(mmvt_hemi_ply_fname) and not op.isfile(mmvt_hemi_npz_fname):
print('{} {}: convert srf to asc'.format(hemi, surf_type))
utils.run_script('mris_convert {} {}'.format(surf_name, surf_wavefront_name))
os.rename(surf_wavefront_name, surf_new_name)
print('{} {}: convert asc to ply'.format(hemi, surf_type))
convert_hemis_srf_to_ply(subject, hemi, surf_type)
if op.isfile(mmvt_hemi_ply_fname):
os.remove(mmvt_hemi_ply_fname)
shutil.copy(hemi_ply_fname, mmvt_hemi_ply_fname)
ply_fname = op.join(MMVT_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type))
if not op.isfile(mmvt_hemi_npz_fname):
verts, faces = utils.read_ply_file(ply_fname)
np.savez(mmvt_hemi_npz_fname, verts=verts, faces=faces)
return utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.pial.ply')) and \
utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.pial.npz')) and \
utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.inflated.ply')) and \
utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.inflated.npz'))
def freesurfer_surface_to_blender_surface(subject, hemi='both', overwrite=False):
for hemi in utils.get_hemis(hemi):
surf_name = op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial'.format(hemi))
surf_wavefront_name = '{}.asc'.format(surf_name)
surf_new_name = '{}.srf'.format(surf_name)
hemi_ply_fname = '{}.ply'.format(surf_name)
mmvt_hemi_ply_fname = op.join(MMVT_DIR, subject, '{}.pial.ply'.format(hemi))
if overwrite or not op.isfile(hemi_ply_fname):
print('{}: convert srf to asc'.format(hemi))
utils.run_script('mris_convert {} {}'.format(surf_name, surf_wavefront_name))
os.rename(surf_wavefront_name, surf_new_name)
print('{}: convert asc to ply'.format(hemi))
convert_hemis_srf_to_ply(subject, hemi)
for hemi in utils.get_hemis(hemi):
if not op.isfile(mmvt_hemi_ply_fname):
shutil.copy(hemi_ply_fname, mmvt_hemi_ply_fname)
ply_fname = op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial.ply'.format(hemi))
verts, faces = utils.read_ply_file(ply_fname)
np.savez(op.join(SUBJECTS_DIR, subject, 'mmvt', '{}.pial'.format(hemi)), verts=verts, faces=faces)
shutil.copyfile(op.join(SUBJECTS_DIR, subject, 'mmvt', '{}.pial.npz'.format(hemi)),
op.join(MMVT_DIR, subject, '{}.pial.npz'.format(hemi)))
return utils.both_hemi_files_exist(op.join(SUBJECTS_DIR, subject, 'surf', '{hemi}.pial.ply'))
def convert_perecelated_cortex(subject, aparc_name, overwrite_ply_files=False, hemi='both'):
lookup = {}
for hemi in utils.get_hemis(hemi):
lookup[hemi] = create_labels_lookup(subject, hemi, aparc_name)
if len(lookup[hemi]) == 0:
continue
srf_fol = op.join(SUBJECTS_DIR, subject,'{}.pial.{}'.format(aparc_name, hemi))
ply_fol = op.join(SUBJECTS_DIR, subject,'{}_{}_ply'.format(aparc_name, hemi))
blender_fol = op.join(MMVT_DIR, subject,'{}.pial.{}'.format(aparc_name, hemi))
utils.convert_srf_files_to_ply(srf_fol, overwrite_ply_files)
rename_cortical(lookup, srf_fol, ply_fol)
utils.rmtree(blender_fol)
shutil.copytree(ply_fol, blender_fol)
return lookup
def convert_perecelated_cortex(subject, aparc_name, surf_type='pial', overwrite_ply_files=False, hemi='both'):
lookup = {}
for hemi in utils.get_hemis(hemi):
lookup[hemi] = create_labels_lookup(subject, hemi, aparc_name)
if len(lookup[hemi]) == 0:
continue
srf_fol = op.join(SUBJECTS_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
ply_fol = op.join(SUBJECTS_DIR, subject,'{}_{}_{}_ply'.format(aparc_name, surf_type, hemi))
blender_fol = op.join(MMVT_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
utils.convert_srf_files_to_ply(srf_fol, overwrite_ply_files)
rename_cortical(lookup, srf_fol, ply_fol)
if surf_type == 'inflated':
for ply_fname in glob.glob(op.join(ply_fol, '*.ply')):
verts, faces = utils.read_ply_file(ply_fname)
verts_offset = 5.5 if hemi == 'rh' else -5.5
verts[:, 0] = verts[:, 0] + verts_offset
utils.write_ply_file(verts, faces, ply_fname)
utils.rmtree(blender_fol)
shutil.copytree(ply_fol, blender_fol)
return lookup
def convert_perecelated_cortex(subject, aparc_name, surf_type='pial', overwrite_ply_files=False, hemi='both'):
lookup = {}
for hemi in utils.get_hemis(hemi):
lookup[hemi] = create_labels_lookup(subject, hemi, aparc_name)
if len(lookup[hemi]) == 0:
continue
srf_fol = op.join(SUBJECTS_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
ply_fol = op.join(SUBJECTS_DIR, subject,'{}_{}_{}_ply'.format(aparc_name, surf_type, hemi))
blender_fol = op.join(MMVT_DIR, subject,'{}.{}.{}'.format(aparc_name, surf_type, hemi))
utils.convert_srf_files_to_ply(srf_fol, overwrite_ply_files)
rename_cortical(lookup, srf_fol, ply_fol)
if surf_type == 'inflated':
for ply_fname in glob.glob(op.join(ply_fol, '*.ply')):
verts, faces = utils.read_ply_file(ply_fname)
verts_offset = 5.5 if hemi == 'rh' else -5.5
verts[:, 0] = verts[:, 0] + verts_offset
utils.write_ply_file(verts, faces, ply_fname)
utils.rmtree(blender_fol)
shutil.copytree(ply_fol, blender_fol)
return lookup
def freesurfer_surface_to_blender_surface(subject, hemi='both', overwrite=False):
# verts, faces = {}, {}
for hemi in utils.get_hemis(hemi):
utils.make_dir(op.join(MMVT_DIR, subject, 'surf'))
for surf_type in ['inflated', 'pial']:
surf_name = op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}'.format(hemi, surf_type))
surf_wavefront_name = '{}.asc'.format(surf_name)
surf_new_name = '{}.srf'.format(surf_name)
hemi_ply_fname = '{}.ply'.format(surf_name)
mmvt_hemi_ply_fname = op.join(MMVT_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type))
mmvt_hemi_npz_fname = op.join(MMVT_DIR, subject, 'surf', '{}.{}.npz'.format(hemi, surf_type))
if overwrite or not op.isfile(mmvt_hemi_ply_fname) and not op.isfile(mmvt_hemi_npz_fname):
print('{}: convert srf to asc'.format(hemi))
utils.run_script('mris_convert {} {}'.format(surf_name, surf_wavefront_name))
os.rename(surf_wavefront_name, surf_new_name)
print('{}: convert asc to ply'.format(hemi))
convert_hemis_srf_to_ply(subject, hemi, surf_type)
# if surf_type == 'inflated':
# verts, faces = utils.read_ply_file(hemi_ply_fname)
# verts_offset = 5.5 if hemi == 'rh' else -5.5
# verts[:, 0] = verts[:, 0] + verts_offset
# utils.write_ply_file(verts, faces, '{}_offset.ply'.format(surf_name))
if op.isfile(mmvt_hemi_ply_fname):
os.remove(mmvt_hemi_ply_fname)
shutil.copy(hemi_ply_fname, mmvt_hemi_ply_fname)
ply_fname = op.join(MMVT_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type))
if not op.isfile(mmvt_hemi_npz_fname):
verts, faces = utils.read_ply_file(ply_fname)
np.savez(mmvt_hemi_npz_fname, verts=verts, faces=faces)
# verts[hemi], faces[hemi] = utils.read_ply_file(mmvt_hemi_npz_fname)
# if not op.isfile(op.join(MMVT_DIR, subject, 'cortex.pial.npz')):
# faces['rh'] += np.max(faces['lh']) + 1
# verts_cortex = np.vstack((verts['lh'], verts['rh']))
# faces_cortex = np.vstack((faces['lh'], faces['rh']))
# utils.write_ply_file(verts_cortex, faces_cortex, op.join(MMVT_DIR, subject, 'cortex.pial.ply'))
# np.savez(op.join(MMVT_DIR, subject, 'cortex.pial.npz'), verts=verts_cortex, faces=faces_cortex)
return utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.pial.ply')) and \
utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.pial.npz')) and \
utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.inflated.ply')) and \
utils.both_hemi_files_exist(op.join(MMVT_DIR, subject, 'surf', '{hemi}.inflated.npz'))
def convert_hemis_srf_to_ply(subject, hemi='both', surf_type='pial'):
for hemi in utils.get_hemis(hemi):
ply_file = utils.srf2ply(op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.srf'.format(hemi, surf_type)),
op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type)))
utils.make_dir(op.join(MMVT_DIR, subject))
def convert_hemis_srf_to_ply(subject, hemi='both'):
for hemi in utils.get_hemis(hemi):
ply_file = utils.srf2ply(op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial.srf'.format(hemi)),
op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial.ply'.format(hemi)))
utils.make_dir(op.join(MMVT_DIR, subject))
shutil.copyfile(ply_file, op.join(MMVT_DIR, subject, '{}.pial.ply'.format(hemi)))
def convert_hemis_srf_to_ply(subject, hemi='both', surf_type='pial'):
for hemi in utils.get_hemis(hemi):
ply_file = utils.srf2ply(op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.srf'.format(hemi, surf_type)),
op.join(SUBJECTS_DIR, subject, 'surf', '{}.{}.ply'.format(hemi, surf_type)))
utils.make_dir(op.join(MMVT_DIR, subject))