def test_ni_parcellate_mult_conn_comps(clust_type):
"""
Test for ni_parcellate with multiple connected components
"""
import tempfile
base_dir = str(Path(__file__).parent/"examples")
out_dir = f"{base_dir}/outputs/sub-25659/ses-1/func"
tmpdir = tempfile.TemporaryDirectory()
k = 150
if clust_type != 'ncut':
local_corr = 'allcorr'
else:
local_corr = 'tcorr'
clust_mask = f"{base_dir}/miscellaneous/pDMN_3_bin.nii.gz"
mask = f"{base_dir}/BIDS/sub-25659/ses-1/anat/sub-25659_desc-brain_" \
f"mask.nii.gz"
func_file = f"{base_dir}/BIDS/sub-25659/ses-1/func/sub-25659_ses-1_task-" \
f"rest_space-MNI152NLin6Asym_desc-" \
f"smoothAROMAnonaggr_bold_short.nii.gz"
conf = f"{base_dir}/BIDS/sub-25659/ses-1/func/" \
f"sub-25659_ses-1_task-rest_desc-confounds_regressors.tsv"
func_img = nib.load(func_file)
nip = clustools.NiParcellate(func_file=func_file, clust_mask=clust_mask,
k=k, clust_type=clust_type,
local_corr=local_corr, outdir=out_dir,
conf=conf, mask=mask)
atlas = nip.create_clean_mask()
if not nip.uatlas:
nip.uatlas = f"{tmpdir.name}/clust-{clust_type}_k{str(k)}.nii.gz"
nip._clust_mask_corr_img = nib.load(clust_mask)
nip.create_local_clustering(overwrite=True, r_thresh=0.4)
out_path = f"{str(tmpdir.name)}/parc_tmp.nii.gz"
parcellation = clustools.parcellate(func_img, local_corr,
clust_type, nip._local_conn_mat_path,
nip.num_conn_comps,
nip._clust_mask_corr_img,
nip._standardize,
nip._detrending, nip.k, nip._local_conn,
nip.conf, tmpdir.name,
nip._conn_comps)
nib.save(parcellation, out_path)
assert atlas is not None
assert os.path.isfile(out_path)
def test_ni_parcellate(clust_type):
"""
Test for ni_parcellate
"""
import tempfile
k = 20
base_dir = str(Path(__file__).parent/"examples")
out_dir = f"{base_dir}/outputs/sub-25659/ses-1/func"
tmpdir = tempfile.TemporaryDirectory()
if clust_type != 'ncut':
local_corr = 'allcorr'
else:
local_corr = 'tcorr'
clust_mask = f"{base_dir}/miscellaneous/rMFG_node6mm.nii.gz"
mask = f"{base_dir}/BIDS/sub-25659/ses-1/anat/sub-25659_desc-brain_" \
f"mask.nii.gz"
func_file = f"{base_dir}/BIDS/sub-25659/ses-1/func/sub-25659_ses-1_" \
f"task-rest_space-MNI152NLin6Asym_desc-" \
f"smoothAROMAnonaggr_bold_short.nii.gz"
func_img = nib.load(func_file)
nip = clustools.NiParcellate(func_file=func_file, clust_mask=clust_mask,
k=k, clust_type=clust_type,
local_corr=local_corr, outdir=out_dir,
conf=None, mask=mask)
atlas = nip.create_clean_mask()
nip.create_local_clustering(overwrite=True, r_thresh=0.4)
out_path = f"{str(tmpdir.name)}/parc_tmp.nii.gz"
parcellation = clustools.parcellate(func_img, local_corr,
clust_type, nip._local_conn_mat_path,
nip.num_conn_comps,
nip._clust_mask_corr_img,
nip._standardize,
nip._detrending, nip.k, nip._local_conn,
nip.conf, tmpdir.name,
nip._conn_comps)
nib.save(parcellation, out_path)
assert out_path is not None
assert atlas is not None