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Bug 3454 - Function in NIRS tutotial 'ft_nirs_transform_ODs' cannot be found because the path is not added

Reported 2018-09-26 09:38:00 +0200
Modified 2019-08-10 12:36:57 +0200
Product: FieldTrip
Component: documentation
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P5 normal
Assigned to: A Huiskamp
Depends on:
See also:

A Huiskamp - 2018-09-26 09:38:12 +0200

The function in the NIRS tutorial 'ft_nirs_transform_ODs(cfg, data);' cannot be found, because the subfolder 'external -> artenis' is not added to the path.

Jan-Mathijs Schoffelen - 2018-10-08 09:19:33 +0200

Are you referring to the single channel or to the multi channel tutorial? Please feel free to add a small section to the tutorial which specifies how to add the required toolbox to the path.

A Huiskamp - 2018-10-08 09:46:01 +0200

The problem is in both tutorials, it is in the part called: 'Transform to changes in oxyHB/deoxyHB' and 'Transform optical densities to oxy- and deoxyhemoglobin concentration changes' in the single and multi channel tutorial, respectively. The code is a bit different in both tutorials, but at the bottom it says 'data_conc = ft_nirs_transform_ODs(cfg, data);' (or 'data_trans = ft_nirs_transform_ODs(cfg, data_sci);' in the multi channel'). The function 'ft_nirs_transform_ODs' cannot be found because of the missing folder.

Jan-Mathijs Schoffelen - 2018-10-08 09:48:02 +0200

How do you suggest to fix this (both in terms of what should be done, and who is going to do this)? I think that from a didactical point of view, the setting of the paths should be explained in the tutorial(s). And from a didactical point of view, it would be good if you did this. That is, if you have editing permissions for the tutorial, but that is the idea of a wiki, isn't it?

A Huiskamp - 2018-10-08 10:15:43 +0200

What has to be done is that the function either needs to be moved in the folder, or the correct folder has to be added to the path. As for who should do it, I don't know. I do not work with the fieldtrip toolbox, I was just exploring its functions out of curiosity. This is why I didn't want to edit it, as I'm not familiar with its customs. Unfortunately I do not have the time to delve into the fieldtrip tutorials and code, but didn't want to ignore a mistake in the tutorial. I hope you can find someone who can edit it so others won't get stuck as wel. Sorry for not being able to help.

Jan-Mathijs Schoffelen - 2018-10-08 10:23:05 +0200


Jan-Mathijs Schoffelen - 2018-10-08 10:23:55 +0200

Sorry Joseph, you accidentally, and unintentionally ended up on the CC list. It won't happen again.

Robert Oostenveld - 2019-08-10 12:36:57 +0200

This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue on