BUG:ROI merge creates index mismatches and inconsistent stat fields in Fall.mat

[senioralmog93]

Describe the issue:

Hi,
I am seeing two related issues that seem to come from the ROI merge logic in Suite2p.

1. ROI merge in the GUI throws an index error

When merging ROIs in the GUI I occasionally get:

IndexError: index XXXX is out of bounds for axis 0 with size YYYY

This happens inside merge_activity_masks, where the merged ROI tries to reference traces using an index that no longer exists.

2. stat becomes inconsistent after running Suite2p

In the resulting Fall.mat, most ROIs have the full set of fields (including xext, yext, neuropil_mask),
but several ROIs created or modified around merge operations are missing these fields.

This results in a stat list where some entries have fewer fields than others, which causes failures in downstream analysis.

Observation

Both issues appeared in the same datasets and seem to point to a shared root cause:
ROI merge operations do not fully update all ROI metadata and indices.

Question

Is this a known issue with the ROI merge/update pipeline?
And is there a recommended workaround to ensure that merged ROIs have consistent indices and complete metadata?

Happy to provide a small example or Fall.mat snippet if needed.

Thanks!

Reproduce the code example:

IndexError: index XXXX is out of bounds for axis 0 with size YYYY

Example input dataset used to reproduce the issue:

No response

Error message:

Version information:

0.14.4

Context for the issue:

No response