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Bug 2823 - restructure the visualisation tutorial

Reported 2015-02-02 14:52:00 +0100
Modified 2018-03-10 21:36:21 +0100
Product: FieldTrip
Component: documentation
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P5 normal
Assigned to:
Depends on:
See also:

Robert Oostenveld - 2015-02-02 14:52:33 +0100

as discussed in the FT meeting. The starting point is the "script" fieldtrip/test/test_tutorial_plotting.m and the data in /home/common/matlab/fieldtrip/data/ftp/tutorial/plotting/ Please try to reproduce that. Once that is conformed, please start editing to create three sections (channel, volumetric, surface). Subsequently I suggest you start to work on the volumetric section, taking inspiration from the channel section.

Remco Bastiaannet - 2015-02-11 17:50:06 +0100

Nietzsche, can you make sure to upload your volume pos-freq-time data to the cluster so I can use it for this tutorial? Thank you! Remco

- 2015-02-11 18:16:12 +0100

Just uploaded it to /home/common/matlab/fieldtrip/data/ftp/tutorial/plotting/ :)

- 2015-02-11 18:16:56 +0100

right, it's called "pos_freq_time". I'll leave you with the job of finding a more suited name for the tutorial.

Robert Oostenveld - 2015-02-12 09:30:32 +0100

I just solved bug 2820, which had to do with interpolating and plotting volumetric source-level data onto a surface. I also wrote a self-contained test script which you might find useful. See test_bug2820.m in fieldtrip/test or have a look here

Robert Oostenveld - 2015-03-02 18:13:24 +0100

just for reference, I suggested to Remco to add some short screen capture movies. Perhaps this is useful (in case you have a mac)

Robert Oostenveld - 2015-03-03 09:23:48 +0100

Created attachment 706 demo gif - full screen (In reply to Robert Oostenveld from comment #5) I tried it with a screen recording of my full screen while I was opening the fieldtrip home page. The original resolution is way too high ar 2560x1600 @60Hz ffmpeg -i -s 600x400 -pix_fmt rgb24 -f gif - | gifsicle --optimize=3 --delay=3 > out.gif mac011> ls -lh out.gif -rw-r--r--@ 1 roboos staff 17M Mar 2 18:06 % original -rw-r--r--@ 1 roboos staff 1.5M Mar 3 09:07 out.gif % output The 1.5 MB is quite OK at 600x400 and the original refresh rate (the gif has almost 900 frames). The refresh rate could be lower (say 20 Hz) and for the wiki it would suffice to have 400x300 for a large figure and 300x200 for a small one. Here is a smaller one ffmpeg -i -s 400x300 -pix_fmt rgb24 -r 20 -f gif - | gifsicle --optimize=3 --delay=9 > out.gif mac011> ls -lh out.gif -rw-r--r--@ 1 roboos staff 469K Mar 3 09:18 out.gif Let me attach this one as demo. It is a bit stretched (the aspect ratio does not match the original). Had it not been for downsampling from 2560 to 300, then I think it would have looked quite ok. Lesson learned: I should start with a MATLAB figure that has the correct pixel dimensions. I would not mind making the gifs on my computer, now that I know how it works. You still would have to share the data and script with me.

- 2015-07-15 17:06:49 +0200

Assessed the situation of the plotting tutorial, and any related bugs, this is the current plan The tutorial lacks information on % TFR data 1. pos_freq_data (without interpolation) - DONE 2. pos_freq_data (interpolated, using same data as 1) - currently it uses a separate data set. Using the same data would make it easier for users to understand This is related to bug 2516 - and is currently in progress. % ERF data 3. plotting source-level ERF data (MNE) 4. channel-level connectivity - there was some old code that worked, but the figure was suboptimal 5. Videos for using the interactive mode at the sensor-level In general, the text and various sections should be restructured such that it reads smoothly, and that there is a similar structure for channel and source level data.

Robert Oostenveld - 2017-05-16 16:58:14 +0200

I march we had a data visualization workshop at the Donders Institute. See As part of that, the plotting tutorial was revised. I suggest that for now we keep it as it is, unless someone else wants to work on it.