mne-tools / mne-tools/mne-python

Issues computing connectivity with CTF system

Open
#6,069 10 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

BUG
Dominant language
Python
Stars
3.5k
Forks
1.6k
Avg merge
1d 6h
Merged PRs (30d)
100

Description

I got a report that the connectivity computation was problematic. If you have a CTF-270 system, the function find_ch_connectivity gives you the connectivity of the CTF-275 system. Code to reproduce:

import mne
from mne.channels import find_ch_connectivity

contrast = mne.evoked.read_evokeds('./S1_discrimination_conds-ave.fif',
                                   condition='contrast_RP', verbose=None)

connectivity, ch_names = find_ch_connectivity(contrast.info, ch_type='mag')
assert connectivity.shape[-1] == len(contrast.info['ch_names'])

here is the file: https://www.dropbox.com/s/bae8rjdu068ws14/S1_discrimination_conds-ave.fif?dl=0.

My suggestion would be to make _compute_ch_connectivity public and deprecate the find_ch_connectivity function. The guesswork in the function introduces more problems than solves.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the report with the linked FIF file and inspect find_ch_connectivity and _compute_ch_connectivity in mne/channels/channels.py. Compare the computed connectivity and channel count for the CTF-270 data, then determine whether exposing the internal function and deprecating find_ch_connectivity is appropriate. Done means the CTF-270 computation no longer uses the wrong system assumptions and the reported shape remains correct.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api, data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.