egi2besa2fieldtrip - topoplot layout
Virginie van Wassenhove
vvw at CALTECH.EDU
Wed Jun 27 18:11:17 CEST 2007
Hi Christian,
yes using cfg.rotate = 0 works fine (see below code I have been
using). Basically rotating by 90 degrees from the configuration
specified in fieldtrip. With this code, com and scale are added to the layout.
cfg = [];
cfg.rotate = 0;
cfg.elecfile = 'C:\Documents and Settings\Virginie\My
Documents\EEG_analysis\CHANNELS_specs\fieldtrip_GSN128.sfp';
egilay = prepare_layout(cfg);
vv
At 04:40 AM 6/27/2007, you wrote:
>Hi Virginie & Olga,
>
>I have just done some tests using the PREPARE_LAYOUT function and
>EGI files and the code seems to behave as it should. If you specify
>cfg.rotate = 0 then the sensor positions come out with the nose
>pointing upwards. Since the default specified in the code is
>cfg.rotate = 90, not specifying cfg.rotate or setting cfg.rotate =
>90 leaves you with the nose pointing to the right.
>
>I would be grateful if you can confirm using your own files that
>PREPARE_LAYOUT with cfg.rotate = 0 works as described above.
>
>Many Thanks,
>Christian
>
>
>On 20 Jun 2007, at 18:29, Virginie van Wassenhove wrote:
>
>>Hi Olga,
>>
>>thanks for your help, I think I got it working now!
>>
>>Virginie
>>
>>At 06:20 AM 6/20/2007, Olga Sysoeva wrote:
>>>Dear Virginie,
>>>
>>>I had the same problem.
>>>Actually, I not understand where the problem comes from, but solve it by
>>>multiplying the coordinates by cos (- 90) and sin (90). See the script
>>>below.
>>>It works good for my data...
>>>
>>>Best Regards,
>>>Olga.
>>>
>>>
>>>%prepare layout
>>>data.elec =
>>>read_fcdc_elec('C:\MATLAB7\work\fieldtrip-20070409\GSN64sag1.sfp');
>>>cfg = [];
>>>cfg.rotate = 90;
>>>cfg.elecfile = 'C:\MATLAB7\work\fieldtrip-20070409\GSN64sag1.sfp';
>>>mylay2 = prepare_layout(cfg);
>>>
>>>for i=1:69
>>> mylay2.width (i)= 0.5
>>>end;
>>>
>>>for i=1:69
>>> mylay2.height (i)= 0.5
>>>end;
>>>
>>>x=mylay.pos (:,1);
>>>y=mylay.pos (:,2);
>>>mylay2.pos (:,1)=y;
>>>mylay2.pos (:,2)=-x;
>>>
>>>
>>>-----Original Message-----
>>>From: FieldTrip discussion list
>>>[<mailto:FIELDTRIP at NIC.SURFNET.NL>mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>>>Of Virginie van Wassenhove
>>>Sent: Tuesday, June 19, 2007 10:38 PM
>>>To: <mailto:FIELDTRIP at NIC.SURFNET.NL>FIELDTRIP at NIC.SURFNET.NL
>>>Subject: [FIELDTRIP] egi2besa2fieldtrip - topoplot layout
>>>
>>>Hi Fieldtripers,
>>>
>>>below find the relevant sample code I am using to plot cluster
>>>results with Fieldtrip release v. 20070514 (latest?).
>>>
>>>I have read previous posts in the discussion but I still bump into
>>>this issue (not sure how old the discussions were).
>>>The recordings were made with an egi system and preprocessed in besa.
>>>Although I am using the prepare_layout function, the layout in
>>>topoplotER (and other plotting tools) needs to be rotated by
>>>90degrees clockwise.
>>>I have tried to use cfg.rotate (in the for loop below, commented
>>>here) but that does not change anything.
>>>
>>>Do you have any suggestions on how to overcome this problem?
>>>Thanks in advance for your help!
>>>
>>>Virginie
>>>
>>>% ==== plot results ====
>>>cfg = [];
>>>cfg.elecfile = '\CHANNELS_specs\fieldtrip_GSN128.sfp';
>>>egilay = prepare_layout(cfg);
>>>
>>>diff_gdav = ill_gdav;
>>>diff_gdav.av = ill_gdav.avg-noill_gdav.avg;
>>>
>>>figure;
>>>% if cfg.latency = [0.3 0.8]; in cluster analysis
>>>%j = [0:0.025:0.5]; % (s), 0 = 1st onset
>>>%m = [1:12:251]; % (samples)
>>>% if cfg.latency = 'all'; in clusteranalysis
>>>j = [0:0.05:1.1]; % (s), 0 = -300ms from1st
>>>onset
>>>m = [1:25:551]; % (samples)
>>>
>>>pos = stat.posclusterslabelmat == 1; % + clusters
>>>neg = (stat.negclusterslabelmat == 1)*(-1); % - clusters
>>>
>>>for k = 1:length(j)-1; % 20 subplots
>>> subplot(4,5,k);
>>> cfg = [];
>>> cfg.xlim=[j(k) j(k+1)];
>>> cfg.zlim=[-3 3];
>>> pos_int = mean(pos(:,m(k):m(k+1))')';
>>> neg_int = mean(neg(:,m(k):m(k+1))')';
>>> cfg.highlight = find(pos_int ==1 | neg_int == -1);
>>> cfg.comment = 'xlim';
>>> cfg.commentpos = 'title';
>>> cfg.layout = egilay;
>>> %cfg.rotate =[90]; % ?? rotate by 90
>>>degrees clock-wise
>>> topoplotER(cfg,diff_gdav);
>>>end
>>>% ====================
>>>
>>>Virginie van Wassenhove, PhD
>>>
>>>:::::::::::: contact info :::::::::::::
>>>Caltech - Division of Biology
>>>1200 E. California Blvd M/C 139-74
>>>Pasadena CA 91125 USA
>>>:::::::::::::::::::::::::::::::::::::::::::::::::
>>><mailto:vvw at caltech.edu>vvw at caltech.edu
>>><mailto:Virginie.van.Wassenhove at gmail.com>Virginie.van.Wassenhove at gmail.com
>>>W: 626.395.8959
>>><http://www.its.caltech.edu/~vvw>http://www.its.caltech.edu/~vvw
>>>
>>>:::::::::::::::::: extras ::::::::::::::::::::
>>><http://www.kiva.org>http://www.kiva.org
>>>http://www.thehungersite.com/
>>><http://www.agloco.com/r/BBBS1539>http://www.agloco.com/r/BBBS1539
>>>:::::::::::::::::::::::::::::::::::::::::::::::::
>>>
>>>----------------------------------
>>>The aim of this list is to facilitate the discussion between users of the
>>>FieldTrip toolbox, to share experiences and to discuss new ideas for MEG
>>>and EEG analysis. See also
>>><http://listserv.surfnet.nl/archives/fieldtrip.html>http://listserv.surfnet.nl/archives/fieldtrip.html
>>>and
>>><http://www.ru.nl/fcdonders/fieldtrip>http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>----------------------------------
>>>The aim of this list is to facilitate the discussion between users
>>>of the FieldTrip toolbox, to share experiences and to discuss new
>>>ideas for MEG and EEG analysis. See also
>>><http://listserv.surfnet.nl/archives/fieldtrip.html>http://listserv.surfnet.nl/archives/fieldtrip.html
>>>and <http://www.ru.nl/fcdonders/fieldtrip>http://www.ru.nl/fcdonders/fieldtrip.
>>
>>Virginie van Wassenhove, PhD
>>
>>:::::::::::: contact info :::::::::::::
>>Caltech - Division of Biology
>>1200 E. California Blvd M/C 139-74
>>Pasadena CA 91125 USA
>>:::::::::::::::::::::::::::::::::::::::::::::::::
>><mailto:vvw at caltech.edu>vvw at caltech.edu
>><mailto:Virginie.van.Wassenhove at gmail.com>Virginie.van.Wassenhove at gmail.com
>>W: 626.395.8959
>><http://www.its.caltech.edu/~vvw>http://www.its.caltech.edu/~vvw
>>
>>:::::::::::::::::: extras ::::::::::::::::::::
>><http://www.kiva.org>http://www.kiva.org
>>http://www.thehungersite.com/
>><http://www.agloco.com/r/BBBS1539>http://www.agloco.com/r/BBBS1539
>>:::::::::::::::::::::::::::::::::::::::::::::::::
>>
>>----------------------------------
>>The aim of this list is to facilitate the discussion between users
>>of the FieldTrip toolbox, to share experiences and to discuss new
>>ideas for MEG and EEG analysis. See also
>><http://listserv.surfnet.nl/archives/fieldtrip.html>http://listserv.surfnet.nl/archives/fieldtrip.html
>>and <http://www.ru.nl/fcdonders/fieldtrip>http://www.ru.nl/fcdonders/fieldtrip.
>
>----------------------------------------------------------------------
>Christian Hesse, PhD, MIEEE
>
>F.C. Donders Centre for Cognitive Neuroimaging
>P.O. Box 9101
>NL-6500 HB Nijmegen
>The Netherlands
>
>Tel.: +31 (0)24 36 68293
>Fax: +31 (0)24 36 10989
>
>Email: <mailto:c.hesse at fcdonders.ru.nl>c.hesse at fcdonders.ru.nl
>Web: <http://www.fcdonders.ru.nl>www.fcdonders.ru.nl
>----------------------------------------------------------------------
>
>
>
>
>----------------------------------
>
>The aim of this list is to facilitate the discussion between users
>of the FieldTrip toolbox, to share experiences and to discuss new
>ideas for MEG and EEG analysis.
>
>http://listserv.surfnet.nl/archives/fieldtrip.html
>
>http://www.ru.nl/fcdonders/fieldtrip/
Virginie van Wassenhove, PhD
:::::::::::: contact info :::::::::::::
Caltech - Division of Biology
1200 E. California Blvd M/C 139-74
Pasadena CA 91125 USA
:::::::::::::::::::::::::::::::::::::::::::::::::
vvw at caltech.edu
Virginie.van.Wassenhove at gmail.com
W: 626.395.8959
http://www.its.caltech.edu/~vvw
:::::::::::::::::: extras ::::::::::::::::::::
http://www.kiva.org
http://www.thehungersite.com/
http://www.agloco.com/r/BBBS1539
:::::::::::::::::::::::::::::::::::::::::::::::::
----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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