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Bug 2903 - replace the FT findcluster function with the refactored version from LIMO
| Status | CLOSED WONTFIX |
| Reported | 2015-05-28 16:34:00 +0200 |
| Modified | 2018-11-12 11:35:02 +0100 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P5 enhancement |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Robert Oostenveld - 2015-05-28 16:34:20 +0200
The LIMO version (which starts off from my implementation) is about 2x faster for the clustering. See https://github.com/LIMO-EEG-Toolbox/limo_eeg and https://github.com/LIMO-EEG-Toolbox/limo_cluster_test
Robert Oostenveld - 2015-05-28 16:34:59 +0200
it is important to check that the input and output variables are exactly the same, otherwise some small changes might be needed.
Eelke Spaak - 2015-05-29 10:58:51 +0200
In the current FT version, a lot of the heavy lifting in findcluster() is done by a mex-file combineClusters (if available). It would be great if we can do it even faster by just using matlab code, but it's worth checking that the mex-file is actually being used when doing benchmarking (as an m-file fallback is also available). Also, there are two general cases of clustering: (1) across channels, which is an irregular dimension requiring neighbourhood structure; and (2) only across regular dimensions. These two might result in different decisions as to which code is fastest.