Broken link in the fittedtemplate example

[contsili]

The fittedtemplate example documentation has a broken link. I believe this is the correct link that contains the function used by prepare_mesh_fittemplate

[contsili]

Why don't we include this function in FT by default?
EEGLAB does that with a lot of plugins.

[schoffelen]

hmm, I don't see where the link should be inserted in the website. Do you perhaps mean that it should be changed in ft_hastoolbox @contsili ?

[contsili]

This is the line in the website with the broken link: ''This requires an external toolbox, which can be downloaded {here}(https://sites.google.com/site/myronenko/research/cpd)''.

[contsili]

Do you perhaps mean that it should be changed in ft_hastoolbox @contsili ?

Yes we should also change ft_hastoolbox.

But my suggestion is more like: why don't we have a webpage in FT where we put all the plugins/external toolboxes? Then we avoid external links that we cannot control and might break in the future. See EEGLAB for inspiration: https://sccn.ucsd.edu/eeglab/plugin_uploader/plugin_list_all.php

[schoffelen]

This is the line in the website with the broken link: ''This requires an external toolbox, which can be downloaded {here}(https://sites.google.com/site/myronenko/research/cpd)''. This is a broken link

Yes I understand, but I could not find the link in the example page that you referenced in the issue.

[robertoostenveld]

we have this https://www.fieldtriptoolbox.org/faq/external/, but it is not automatically updated and quite out of date.

[contsili]

I tag @simonhomoelle who seems to be the one that first introduced CPD in FT.

I cannot find the CPD toolbox by Myrenko anywhere in the web. I only found it in C++ code: https://github.com/gadomski/cpd/tree/main

I see three options here:

1. Use a built-in Matlab function that performs CPD: pcregistercpd.

2. Write our own function that does CPD. I think most of the recipe is here: https://github.com/markeroon/matlab-computer-vision-routines/blob/master/third_party/CPD2/core/cpd_register.m

3. Forget totally about CPD. It seems to not be important for MEG data analysis. I just stepped into it in the fittedtemplate example documentation which is just used as a second method.

To make all these changes we need to update ft_prepare_mesh, prepare_mesh_fittemplate, ft_hastoolbox, the fittedtemplate example doc, and https://www.fieldtriptoolbox.org/faq/external/. Quite some work I would say.

[schoffelen]

I would vote for 2), and put a copy of this file in fieldtrip/external/cpd, it's shared under the GNU2 licence so that would be fine. It would be nice to add a README in external/cpd describing where the included file was obtained (i.e. linking to the github repo). You could perhaps sample some other directories in fieldtrip/external to get some inspiration.