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Bug 890 - create mat-files for the mostly used acquisition systems to better reflect the features of the channel positions/ outline
| Status | CLOSED FIXED |
| Reported | 2011-08-24 13:31:00 +0200 |
| Modified | 2019-08-10 12:03:33 +0200 |
| Product: | FieldTrip |
| Component: | plotting |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P1 enhancement |
| Assigned to: | Arjen Stolk |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Jan-Mathijs Schoffelen - 2011-08-24 13:31:10 +0200
preferably use pictures of the channel layout and use ft_prepare_layout move the old .lay files to an 'old' directory.
Jan-Mathijs Schoffelen - 2011-08-24 13:32:20 +0200
also include the original picture in the mat-file from which the layout was obtained.
Jörn M. Horschig - 2011-08-29 14:13:21 +0200
Since I am working on bug 619, how exactly should that work or look like?
Arjen Stolk - 2011-09-13 16:14:56 +0200
Created attachment 131 32ch easycap
Arjen Stolk - 2011-09-13 16:15:20 +0200
Created attachment 132 64ch easycap
Arjen Stolk - 2011-09-13 16:19:02 +0200
With cfg.img = '*.bmp' and lay = ft_prepare_layout(cfg, []) one can specify the electrode locations and the polygons for topographic interpolation and outlining. The lay structure should be stored in a .mat file, together with the .bmp file. Find attached the bitmaps for the easycaps.
Arjen Stolk - 2011-09-13 16:20:30 +0200
The reference frame (outline) needs discussing. Supposedly, it does not auto-scale?
Jörn M. Horschig - 2011-09-13 17:18:13 +0200
I think you should skip the easycap layouts, because of my bug ;)
Arjen Stolk - 2011-09-14 08:19:20 +0200
hoh hoh I'm not trying to steal bugs here! :D I'll upload more bmp's as soon as I have 'm
Arjen Stolk - 2011-09-28 10:58:23 +0200
Created attachment 139 acticap 64ch
Arjen Stolk - 2011-09-28 11:03:37 +0200
Created attachment 141 acticap 64ch donders
Arjen Stolk - 2011-09-28 11:07:39 +0200
Created attachment 142 acticap 32ch
Arjen Stolk - 2011-09-28 11:07:57 +0200
Created attachment 143 acticap 64ch
Arjen Stolk - 2011-09-28 11:08:13 +0200
Created attachment 144 acticap 128ch
Arjen Stolk - 2011-09-28 11:13:30 +0200
Created attachment 145 BTI/4D 148ch
Arjen Stolk - 2011-09-28 11:13:52 +0200
Created attachment 146 BTI/4D 248ch
Arjen Stolk - 2011-09-28 11:15:44 +0200
Created attachment 148 CTF 275ch
Arjen Stolk - 2011-09-28 17:10:09 +0200
Created attachment 149 CTF 275 matfile containing the lay structure
Arjen Stolk - 2011-09-28 17:18:08 +0200
(In reply to comment #17) > Created attachment 149 [details] > CTF 275 matfile containing the lay structure I've processed the CTF275 layout. The procedure is as follows: 1) specify the bitmap you want to process and call ft_prepare_layout cfg.image = '*.bmp' lay = ft_prepare)layout(cfg) 2) specify the channels tip: after every few electrodes/sensors, write down the names to not make mistakes when you've forgotten the selection sequence, e.g. label = { 'MLF14' 'MLF13' } 3) specify the topographic interpolation boundaries 4) specify the 'head' and sulci outlines 5) copy your label onto the lay structure lay.label = label 6) save the lay file into a matfile; e.g. 'CTF275.mat' and upload it (to here for instance)
Arjen Stolk - 2011-09-29 11:02:06 +0200
Still to find: - biosemi layouts (16,32,64,128,160,256ch) - neuromag layouts (306ch planar, mag, cmb, all) - yokogawa (440ch)
Jörn M. Horschig - 2011-09-29 12:52:33 +0200
I could ask people from the DCC, they are working with BioSemi caps, should I? I know that they got at least got elecs (electrode positions)
Arjen Stolk - 2011-09-29 13:59:47 +0200
That'd be great yes. Oh, we really do want the layouts (figures) to also map the outlines and sulci. The biosemi electode positions are on the resp. website, I believe, just not the figs. Btw, I'm a bit lost on the easycap layouts. The ones you've sent me are different from the ones attached here, right? Do you know which ones we should include in the ft/template dir? (In reply to comment #20) > I could ask people from the DCC, they are working with BioSemi caps, should I? > I know that they got at least got elecs (electrode positions)
Jörn M. Horschig - 2011-09-29 14:14:10 +0200
Hey, the ones I sent you are from the easycap homepage, so these should be the official ones, I guess ;)
Jörn M. Horschig - 2011-10-04 11:10:14 +0200
I just remembered this page: http://www.biosemi.com/headcap.htm should help, shouldn't it?
Jörn M. Horschig - 2011-10-04 13:39:22 +0200
Created attachment 153 Mat-files for easycap layouts M1, M10, M11, M14, M15 and M16 I attached the easycap layouts to this bug instead of bug 619, so that we got them all at one place Still need to do some, but they are mere simplified versions (with fewer electrodes) of the attached ones
Jörn M. Horschig - 2011-10-04 16:30:34 +0200
Created attachment 154 all relevant easycap layouts
Jörn M. Horschig - 2011-10-04 16:42:46 +0200
Created attachment 155 all relevant easycap layouts grm grm... forgot one, now it's 'em all
Jörn M. Horschig - 2011-10-04 16:48:52 +0200
Btw, I used the original FT outline&mask and scaled / moved my electrodes into these - I felt that this was easier, given that I already converted the picture files into a .lay. I could do a similar thing to the CTF275 layouts. That way, the outline will look nicer, because it is based on a 'perfect' circle rather than on human mouse clicks. Also, the nose and the ears will look nicer. Any reason why I should not do it?
Arjen Stolk - 2011-10-04 17:18:38 +0200
Good job! :) The outline is ugly yes, let's discuss tomorrow. (In reply to comment #27) > Btw, I used the original FT outline&mask and scaled / moved my electrodes into > these - I felt that this was easier, given that I already converted the picture > files into a .lay. > I could do a similar thing to the CTF275 layouts. That way, the outline will > look nicer, because it is based on a 'perfect' circle rather than on human > mouse clicks. Also, the nose and the ears will look nicer. Any reason why I > should not do it?
Jörn M. Horschig - 2011-10-19 16:29:12 +0200
the mat files are not ready yet, I guess? I am asking because I am working on bug 890 for which I use layout-files to create neighbour structures. Would be nicer if the templates were already based on the new layout-files (only if we got no 3D data available, of course)
Arjen Stolk - 2011-10-19 16:37:11 +0200
I think none of the layout files are made yet. I was thinking of making one for the CTF275 with a 2d view on the dewar. Are you working on the easycap ones? (In reply to comment #29) > the mat files are not ready yet, I guess? I am asking because I am working on > bug 890 for which I use layout-files to create neighbour structures. Would be > nicer if the templates were already based on the new layout-files (only if we > got no 3D data available, of course)
Arjen Stolk - 2012-02-01 16:03:20 +0100
(In reply to comment #30) The easycap*.mat files and their corresponding images (easycap*.png) have been uploaded to /template/layout
Arjen Stolk - 2012-11-28 17:07:18 +0100
Layouts and their descriptions are now being created on /template/layout. ideally, images are moved from http://fieldtrip.fcdonders.nl/tutorial/layout to http://fieldtrip.fcdonders.nl/template/layout provided a link is given
Arjen Stolk - 2013-01-15 20:10:23 +0100
Current status: - layouts that can refer to an image have been created (with positions and outline based on the image) and stored in a .mat file - all layouts have been documented at the wiki: http://fieldtrip.fcdonders.nl/template/layout - it remains a challenge to create new layouts for the MEG system as proper images are lacking. An attempt for the CTF system, based on the actual 3D positions, is added to the attachments (elproj_CTF275.m and .pdf). - http://fieldtrip.fcdonders.nl/tutorial/layout has been cleaned To do: - clean up fieldtrip/template/layout: there are .lay files of which a .mat file exists (the .lay can be deleted in this case) - clean up ambiguous .lay files (e.g. language29ch-avg.lay and CTF275s.lay) - provide links (on the wiki) to the /template pages (e.g. on http://fieldtrip.fcdonders.nl/tutorial/layout)
Arjen Stolk - 2013-01-15 20:11:21 +0100
Created attachment 400 CTF75 channel projections
Arjen Stolk - 2013-01-15 20:11:45 +0100
Created attachment 401 CTF275 channel projection example script
Arjen Stolk - 2013-01-16 15:43:05 +0100
todo: an overview (table) of the existing layouts, in order to spot the overlaps
Arjen Stolk - 2013-01-16 15:45:21 +0100
Note that (a question raised during the FT meeting today), simply specifying the layout file without the extension will not work (e.g. cfg.layout = 'easycapM1'; ft_prepare_layout(cfg)).
Jörn M. Horschig - 2013-01-16 16:50:14 +0100
can we make it work? shouldn't me much that we need to change, right? if no extension, check whether .mat exists, if not check whether .lay exists
Arjen Stolk - 2013-01-16 17:49:06 +0100
Yep, good suggestion. Will try to sort it out.
Arjen Stolk - 2013-01-23 14:40:23 +0100
Created attachment 412 overview of layouts in template depository
Arjen Stolk - 2013-01-23 14:53:42 +0100
Update: - fieldtrip/template/layout has been cleaned up - an overview of removed files (because duplicate and obsolete), but also up-to-date files can be found in the attached spreadsheet ('overview of layouts in template depository') - Eelke has added the feature to ft_prepare_layout to specify the layout without the need for an extension. e.g. cfg.layout = 'CTF151'; ft_prepare_layout will first try to find and load the corresponding .mat file. If this does not exist, it will try and load the corresponding .lay file - a link to /template/layout has been inserted in /tutorial/layout of the wiki