A surface with χ ≠ 1

[XYWCQM]

Hello, when I was using autoflatten to flatten the cortex, the projection function was working properly. However, when I tried to run the flattening process afterwards, I encountered the following issue:
autoflatten $SUBJECTS_DIR/S6 --output-dir ./flatten
Starting Autoflatten Pipeline...
FreeSurfer version: stable6
Subject: S6
Subject directory: /usr/local/freesurfer/subjects/S6
Output directory: ./flatten
Processing hemispheres: lh, rh

Processing lh hemisphere for subject S6
Patch file ./flatten/lh.autoflatten.patch.3d already exists, skipping (use --overwrite to force)
Using pyflatten backend for flattening
Running pyflatten backend
Input patch: ./flatten/lh.autoflatten.patch.3d
Base surface: /usr/local/freesurfer/subjects/S6/surf/lh.fiducial
Output: ./flatten/lh.autoflatten.flat.patch.3d
K-ring: 7, neighbors/ring: 12
Loading cortical surface patch...
Mesh: 141,323 vertices, 282,642 faces
Error processing lh hemisphere:
Traceback (most recent call last):
File "/home/monkey/anaconda3/lib/python3.10/site-packages/autoflatten/cli.py", line 656, in cmd_run_full_pipeline
results[hemi] = process_hemisphere(
File "/home/monkey/anaconda3/lib/python3.10/site-packages/autoflatten/cli.py", line 486, in process_hemisphere
flat_file = run_flatten_backend(
File "/home/monkey/anaconda3/lib/python3.10/site-packages/autoflatten/cli.py", line 373, in run_flatten_backend
return backend.flatten(
File "/home/monkey/anaconda3/lib/python3.10/site-packages/autoflatten/backends/pyflatten.py", line 166, in flatten
flattener.load_data(patch_path, surface_path)
File "/home/monkey/anaconda3/lib/python3.10/site-packages/autoflatten/flatten/algorithm.py", line 1657, in load_data
euler = validate_topology(
File "/home/monkey/anaconda3/lib/python3.10/site-packages/autoflatten/flatten/algorithm.py", line 245, in validate_topology
raise TopologyError(msg)
autoflatten.flatten.algorithm.TopologyError: Surface has Euler characteristic χ = 2 (expected 1 for disk topology).
Vertices: 141,323, Edges: 423,963, Faces: 282,642
This indicates the surface has topological defects (holes, handles, or disconnected components).
A surface with χ ≠ 1 cannot be flattened to a plane without self-intersections.
Consider using mris_cut to create a disk-like patch, or check the surface for defects.
Could you please tell me how to solve it? I'm looking forward to your reply, thank you.

[mvdoc]

Hi, thank you for the report. This problem means that there are some vertices without faces, or more generally that the automatic cutting procedure didn't work. I'd like to narrow down this issue because I ran autoflatten on 100+ hemispheres and didn't hit this problem.

The automatic cutting process should have generated an image with the template cut projected to the subject's surface: how does that look? And just to be sure, the subject brain is a human brain, correct? (In theory it should support other templates but we only ship code to run against human fsaverage.)

[XYWCQM]

Thank you for your reply. This is the file generated after I ran "autoflatten $SUBJECTS_DIR/S6 --output-dir ./flatten":

autoflatten.zip

Data is human data.