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Bug 2382 - tutorial documentation: improve usability
| Status | CLOSED FIXED |
| Reported | 2013-11-20 14:00:00 +0100 |
| Modified | 2018-03-10 21:35:05 +0100 |
| Product: | FieldTrip |
| Component: | documentation |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P3 normal |
| Assigned to: | |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Jan-Mathijs Schoffelen - 2013-11-20 14:00:41 +0100
TO DO: -restructure the main page of the tutorials a bit: making the subsections more clear by using headings -restructure the individual tutorials to contain a small section that refers to the tutorials that use the same dataset: see realtime documentation\ -add some info for the real beginner, suggestions with which tutorials to start, probably accommodating different backgrounds: EEG/MEG/animal electrophys. -create FAQ: which datasets are used in the tutorials? +linking tutorials +using tags -tagging the tutorials with the dataset used. e.g. meg_language, eeg_somethingelse
- 2013-11-20 19:24:44 +0100
I will get started on the FAQ.
- 2013-11-21 18:36:54 +0100
Created attachment 561 Notes all datasets on FT
- 2013-11-21 18:37:39 +0100
Created attachment 562 excel sheet assigning datasets to tutorials
- 2013-11-21 18:45:35 +0100
Word document: summarises what each dataset is, and also makes notes on things that we should restructure / get consistent across tutorials Excel document: shows which datasets are used in which tutorials. These documents can be updated regularly and easily, I think :) Please, could someone take a look at this, and see if I've missed out any datasets, or if a particular dataset pops right into mind? Next: work on writing the actual FAQ info, and creating FAQ on wiki
Robert Oostenveld - 2013-12-10 15:57:42 +0100
I added a reference to wang et al 2012 to http://fieldtrip.fcdonders.nl/tutorial/shared/dataset. I was not able to get the formatting of the superscript 4 the same as elsewhere on that page for 1, 2, 3. If anyone has an idea?
Robert Oostenveld - 2013-12-10 16:10:56 +0100
Created attachment 573 updated word document I added some comments and pointers to the word document. We better move it over to the FAQ and start working on it there.
- 2013-12-10 16:39:24 +0100
Thanks for the comments Robert, they help clear things up. I've created the FAQ page and will start compiling info for it.
- 2013-12-11 14:58:50 +0100
- #4 - science paper, #6 j. neurosci paper - provide link to paper where possible - automatically generate the list of tutorials: --> place topic at end of each relevant tutorial - get link for paper for #11 from Robert
Robert Oostenveld - 2013-12-11 15:38:09 +0100
(In reply to comment #8) #11 is a recording that was performed with the setup as described in http://www.ncbi.nlm.nih.gov/pubmed/16407546. The subject is indeed obvious from the filename (Bauer). From the description on http://fieldtrip.fcdonders.nl/example/fit_a_dipole_to_the_tactile_erf_after_mechanical_stimulation whichg mentions it as "too hard to distinguish them", I do infer that it was a pilot measurement, i.e. there was no task involved, which means that it was not one of the recordings used in the paper.
- 2013-12-11 15:54:20 +0100
@ Robert - you mentioned adding a topic tag. I tried to hunt for this but I'm still a bit lost. @ Eelke too - is it necessary to have this plugin https://www.dokuwiki.org/plugin:include for the topic tag to work?
Eelke Spaak - 2013-12-11 15:58:55 +0100
(In reply to comment #10) If you have a look at e.g. the source for one of the tutorials, you can see some examples of how to include tags; it's done by using something like {{tag>tutorial qsub peer distcomp matlab}} at the top of the page. Just think of a name for each specific dataset, and add that tag to each page that references it. On the overview page, you can make the list of links like so: {{topic>mytag &list}}
Robert Oostenveld - 2013-12-11 16:01:59 +0100
(In reply to comment #11) please do post the suggested tags here before adding them to the wiki, I'd like to review them.
- 2013-12-11 16:45:03 +0100
(In reply to comment #12) Hi Robert, I was thinking of using the names of the datasets as the tags. However, in order to make the dataset name transparent the names are quite long e.g,: MEG-language-semantics EEG-language-semantics MEG-artifacts MEG-visuomotor- ... etc Please just see the FAQ page for the rest of the names I came up with: http://fieldtrip.fcdonders.nl/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip One option is to shorten the names to e.g., MEG-lang-sem
- 2013-12-11 16:49:28 +0100
i cannot locate the origins of dataset #8 on the FieldTrip website. These are spike recordings of rat hippocampal data as indicated on the tutorial. Might someone have a clue? :)
Robert Oostenveld - 2013-12-11 21:09:51 +0100
(In reply to comment #14) Hi Martin (CC), can you give some details on the spike dataset? A sentences words and potentially a link to a publication would be great. See previous comments if you want to know the context of the question. thanks Robert
Robert Oostenveld - 2013-12-11 21:50:45 +0100
(In reply to comment #13) how about this? (1) MEG-language (2) EEG-semantics (3) MEG-artifact (4) MEG-visuomotor151 (5) MEG-attention (6) MEG-visuomotor275 (please check with 4) (7) LFP-spike-attention (8) Spike/Local Field Potentials-memory-? ?? (9) EEG-TMS-motor (10) MEG-braille
Robert Oostenveld - 2013-12-12 08:58:43 +0100
(In reply to comment #16) perhaps (8) Spike-hippocampus An alternative is to use cryptical names, like "exampledata1", "exampledata2", ...
- 2013-12-12 12:52:18 +0100
(In reply to Robert Oostenveld from comment #16) oops, I didn't see this comment, sorry for not responding. @ Robert, I can see that you want to make the names shorter, which is reasonable, but then I would like to be consistent about the format: (1) MEG-language vs. (2) EEG-semantics is consistent. I would like to the first word to represent what measurement was done, and the second word to reflect what topic. So: (1) MEG-language (2) EEG-language (3) MEG-artifact (4) MEG-visuomotor151 (5) MEG-attention (6) MEG-visuomotor275 (7) Spike-attention (8) Spike-memory % this was the hippocampus one (9) EEG/TMS-motor (10)MEG-perception % braille doesn't quite fit in with the other broad categories
Martin Vinck - 2013-12-18 07:19:38 +0100
(In reply to Robert Oostenveld from comment #15) hi Robert - this is just a standard hippocampal dataset in which a rat runs around on a maze and you gather place fields in CA1. It's one cell from an unpublished dataset.
Robert Oostenveld - 2013-12-19 09:49:58 +0100
(In reply to Martin Vinck from comment #19) thanks Martin. (In reply to n.lam from comment #18) I would do (8) Spike-placefield (10) MEG-tactile Perception and memory are too broad and will most likely conflict with future memory or perception tutorials. Furthermore I am worried about the technical consequences of the slash in EEG/TMS (like URLs breaking etc). How about (9) EEG-TMS for that one?
- 2013-12-23 13:43:43 +0100
(In reply to Jan-Mathijs Schoffelen from comment #0) Some of the things listed on this comment have been completed: TO DO: -restructure the main page of the tutorials a bit: making the subsections more clear by using headings = IN PROGRESS -restructure the individual tutorials to contain a small section that refers to the tutorials that use the same dataset: see realtime documentation = TO BE ASSIGNED -add some info for the real beginner, suggestions with which tutorials to start, probably accommodating different backgrounds: EEG/MEG/animal electrophys. = TO BE ASSIGNED -create FAQ: which datasets are used in the tutorials? +linking tutorials +using tags = COMPLETED -tagging the tutorials with the dataset used. e.g. meg_language, eeg_somethingelse = COMPLETED
- 2013-12-23 13:53:20 +0100
restructuring of main page of tutorials is now completed! :)
Jörn M. Horschig - 2014-01-06 10:36:29 +0100
Hi Nietzsche, happy new year ;) In light of bug 2311, I gotta promote an example script to a tutorial. It's about this example script: http://fieldtrip.fcdonders.nl/example/preprocessing_eeg which uses the same dataset as the continuous preprocessing tut btw: if you set the status of your bugs to 'assigned', you get one mail per day less from the bugzilla page ;)
- 2014-01-06 12:08:31 +0100
(In reply to Jörn M. Horschig from comment #23) Hi Jörn, Guten Rusch! Thanks for the update, I will change the FAQ accordingly. Nietz
- 2014-01-08 11:42:11 +0100
(In reply to Jörn M. Horschig from comment #23) Hey Jörn, You wanted to promote the example script to a tutorial. So does this mean you will update the tutorial page, and also change the link of the script (currently it's still <http://fieldtrip.fcdonders.nl/example/preprocessing_eeg>, but it should be <http://fieldtrip.fcdonders.nl/tutorial/preprocessing_eeg>?) or did you mean that I should do it, as well as update the FAQ?
Jörn M. Horschig - 2014-01-08 12:19:00 +0100
Hi Nietzsche, I'm gonna do that, probably later today, after the FT meeting
- 2014-01-08 12:36:40 +0100
(In reply to Jörn M. Horschig from comment #26) Cool, no rush, just wanted to be sure (since I'm on an FT bug roll). Let me know when you're set, then I'll update accordingly.
- 2014-01-08 14:53:41 +0100
Address the task: -add some info for the real beginner, suggestions with which tutorials to start, probably accommodating different backgrounds: EEG/MEG/animal electrophys. I'll look through what's on 'Getting Started', 'User Documentation', considering content of the walkthrough. Keeping in mind what categories we could form, based on the tutorial and information that we already have on the site Try to provide information for the following groups: - No Matlab Experience (link to page on literature) - MEg interest - EEG interest (incl. ecog) - Animal Physiology -> point towards spike train tutorials Use the "if X, then Y" structure. 'event-related fields', is also spelled as 'event related fields' - would be nice to change the wrong ones
- 2014-01-28 23:43:54 +0100
@ Jörn, I'm reading through the new EEG tutorial and noticed several places that were copy pasted from the corresponding MEG tutorial - I will go through and update it (e.g., places where it says 'MEG" it should say "EEG") if you don't mind? I had to post here because I couldn't find a bug under your name that talks about upgrading the example script into a tutorial. N.
Jörn M. Horschig - 2014-01-29 09:06:51 +0100
sure, feel free ;)