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Remove accidental duplicated streamlines on diagonal #1368

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Merged
arnaudbore merged 1 commit into from
Oct 27, 2026
Merged

Remove accidental duplicated streamlines on diagonal #1368

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6 changes: 6 additions & 0 deletions src/scilpy/cli/tests/test_tractogram_segment_connections_from_labels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
from scilpy.io.streamlines import load_tractogram_with_reference

# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(), keys=['connectivity.zip'])
Expand All @@ -31,3 +32,8 @@ def test_execution_connectivity(script_runner, monkeypatch):
'--save_final', '--out_dir',
os.path.join(tmp_dir.name, 'out_bundles')])
assert ret.success
# Ensure self-connections (i, i) are not duplicated (raw 314, not 628)
sft_9_9 = load_tractogram_with_reference(
None, None,
os.path.join(tmp_dir.name, 'out_bundles', 'final_connections', '9_9.trk'))
assert len(sft_9_9) == 314
2 changes: 1 addition & 1 deletion src/scilpy/tractanalysis/connectivity_segmentation.py
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Expand Up @@ -212,7 +212,7 @@ def construct_hdf5_from_connectivity(
pair_info = []
if out_label in con_info[in_label]:
pair_info.extend(con_info[in_label][out_label])
if in_label in con_info[out_label]:
if in_label != out_label and in_label in con_info[out_label]:
pair_info.extend(con_info[out_label][in_label])
if len(pair_info) == 0:
logging.debug("No streamlines found for this connection: not "
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