multiplotTFR goes wrong
sibylle
s.mohr at PSY.GLA.AC.UK
Mon Nov 9 13:37:45 CET 2009
Dear Robert,
thanks a lot for your reply!
As you suggested, I will give it a try with an old fieldtrip version.
Cheers & best wishes,
Sibylle
On 9 Nov 2009, at 08:22, Robert Oostenveld wrote:
> Dear Sibylle,
>
> Your script looks ok, and I don't recall any changes that might
> relate to the problem that you are describing. Could you try to run
> the script using an old version of fieldtrip, corresponding to the
> original date of your analysis? If the old version and new version
> then indeed produce inconsistent results, you can look at each of
> the individual steps to pinpoint the step in the analysis where it
> goes wrong.
>
> To help you perform the analysis with an older fieldtrip version, I
> have copied some old versions onto the ftp server. All versions of
> fieldtrip-lite-2009??01.zip are now present, i.e. the first day of
> each month. I hope this goes back enough.
>
> best regards,
> Robert
>
>
> On 3 Nov 2009, at 14:30, Sibylle Mohr wrote:
>
>> Dear Fieldtrippers,
>>
>> I have a problem concerning multiplotTFR, which I did not have a
>> couple of months ago:
>> I import 4 conditions (lexical match/lexical mismatch and
>> stereotypical match /
>> stereotypical mismatch). After doing a multitaper analysis for
>> different frequencies I do a
>> baseline correction using 'zscore' across the averaged trials for
>> each condition. When I
>> plot the resulting zscore corrected conditions using multiploTFR
>> contrasting 'lexical
>> mismatch' with 'lexical match' and afterwards 'stereotypical
>> mismatch' with 'stereotypical
>> match', it looks like the stereotypical conditions are almost the
>> inverse plot of my lexical
>> conditions. I always clear the cfg before I start a new plot. I
>> also use cfg.interactive =
>> 'yes'. Any ideas why this is happening..?
>>
>> I'll attach the scripts for the multitaper analysis, the baseline
>> correction, and for the
>> plotting.
>>
>> Thanks,
>>
>> Sibylle
>>
>> -----------------------
>> MULTITAPER ANALYSIS
>>
>> function hifreq_ana
>>
>> % anaphora files: high frequencies
>>
>> % BESA datafiles in one condition
>> filename_ana{1} = {
>> 'An1_sb1_lexmatch-export.dat'
>> 'An1_sb9_lexmatch-export.dat'
>> 'An1_sb13_lexmatch-export.dat'
>> 'An1_sb17_lexmatch-export.dat'
>> 'An1_sb21_lexmatch-export.dat'
>> 'An2_sb2_lexmatch-export.dat'
>> 'An2_sb6_lexmatch-export.dat'
>> 'An2_sb10_lexmatch-export.dat'
>> 'An2_sb18_lexmatch-export.dat'
>> 'An2_sb22_lexmatch-export.dat'
>> 'An3_sb3_lexmatch-export.dat'
>> 'An3_sb7_lexmatch-export.dat'
>> 'An3_sb11_lexmatch-export.dat'
>> 'An3_sb15_lexmatch-export.dat'
>> 'An3_sb23_lexmatch-export.dat'
>> 'An4_sb4_lexmatch-export.dat'
>> 'An4_sb8_lexmatch-export.dat'
>> 'An4_sb12_lexmatch-export.dat'
>> 'An4_sb16_lexmatch-export.dat'
>> 'An4_sb24_lexmatch-export.dat'
>> };
>>
>>
>> % BESA datafiles in the other condition
>> filename_ana{2} = {
>> 'An1_sb1_lexmis-export.dat'
>> 'An1_sb9_lexmis-export.dat'
>> 'An1_sb13_lexmis-export.dat'
>> 'An1_sb17_lexmis-export.dat'
>> 'An1_sb21_lexmis-export.dat'
>> 'An2_sb2_lexmis-export.dat'
>> 'An2_sb6_lexmis-export.dat'
>> 'An2_sb10_lexmis-export.dat'
>> 'An2_sb18_lexmis-export.dat'
>> 'An2_sb22_lexmis-export.dat'
>> 'An3_sb3_lexmis-export.dat'
>> 'An3_sb7_lexmis-export.dat'
>> 'An3_sb11_lexmis-export.dat'
>> 'An3_sb15_lexmis-export.dat'
>> 'An3_sb23_lexmis-export.dat'
>> 'An4_sb4_lexmis-export.dat'
>> 'An4_sb8_lexmis-export.dat'
>> 'An4_sb12_lexmis-export.dat'
>> 'An4_sb16_lexmis-export.dat'
>> 'An4_sb24_lexmis-export.dat'
>> };
>>
>> filename_ana{3} = {
>> 'An1_sb1_stermatch-export.dat'
>> 'An1_sb9_stermatch-export.dat'
>> 'An1_sb13_stermatch-export.dat'
>> 'An1_sb17_stermatch-export.dat'
>> 'An1_sb21_stermatch-export.dat'
>> 'An2_sb2_stermatch-export.dat'
>> 'An2_sb6_stermatch-export.dat'
>> 'An2_sb10_stermatch-export.dat'
>> 'An2_sb18_stermatch-export.dat'
>> 'An2_sb22_stermatch-export.dat'
>> 'An3_sb3_stermatch-export.dat'
>> 'An3_sb7_stermatch-export.dat'
>> 'An3_sb11_stermatch-export.dat'
>> 'An3_sb15_stermatch-export.dat'
>> 'An3_sb23_stermatch-export.dat'
>> 'An4_sb4_stermatch-export.dat'
>> 'An4_sb8_stermatch-export.dat'
>> 'An4_sb12_stermatch-export.dat'
>> 'An4_sb16_stermatch-export.dat'
>> 'An4_sb24_stermatch-export.dat'
>> };
>>
>>
>> % BESA datafiles in the other condition
>> filename_ana{4} = {
>> 'An1_sb1_stermis-export.dat'
>> 'An1_sb9_stermis-export.dat'
>> 'An1_sb13_stermis-export.dat'
>> 'An1_sb17_stermis-export.dat'
>> 'An1_sb21_stermis-export.dat'
>> 'An2_sb2_stermis-export.dat'
>> 'An2_sb6_stermis-export.dat'
>> 'An2_sb10_stermis-export.dat'
>> 'An2_sb18_stermis-export.dat'
>> 'An2_sb22_stermis-export.dat'
>> 'An3_sb3_stermis-export.dat'
>> 'An3_sb7_stermis-export.dat'
>> 'An3_sb11_stermis-export.dat'
>> 'An3_sb15_stermis-export.dat'
>> 'An3_sb23_stermis-export.dat'
>> 'An4_sb4_stermis-export.dat'
>> 'An4_sb8_stermis-export.dat'
>> 'An4_sb12_stermis-export.dat'
>> 'An4_sb16_stermis-export.dat'
>> 'An4_sb24_stermis-export.dat'
>> };
>>
>> ncond = length(filename_ana);
>> nsubj = length(filename_ana{1});
>>
>>
>> tmp = importdata('New_elect72.elp');
>>
>> for j = 1:ncond
>> clear data
>>
>> for i=1:nsubj
>> data = besa2fieldtrip(filename_ana{j}{i});
>> % % import electrode file and create electrode arrays
>> % % with coordinates in elp file
>> % % match channel and electrode names
>> data.label = tmp.textdata(:,2);
>>
>> clear cfg;
>> cfg.foi = [30:4:130];
>> numfoi = length(cfg.foi);
>> cfg.t_ftimwin = zeros(1,numfoi);
>> cfg.t_ftimwin(:) = 0.25;
>> cfg.method = 'mtmconvol';
>> cfg.output = 'pow';
>> cfg.toi = [-0.5:0.02:1.5];
>> cfg.taper = 'dpss';
>> cfg.tapsmofrq = zeros(1,numfoi);
>> cfg.tapsmofrq(:) = 16;
>> cfg.keeptrials = 'yes';
>>
>> freqhi = freqanalysis(cfg,data);
>> % change from double to single precision to save space on the
>> harddisk
>> single = struct2single(freqhi);
>> save(sprintf('/analyse/12/Project0042/Gender_new/dat-
>> files_multitaper/anaphora/hi_freq_%d_%d.mat',j,i),'single');
>> clear single
>>
>> end; % subject loop
>> end; % condition loop
>> exit;
>> ---------------------------------------
>>
>> BASELINE CORRECTION SCRIPT
>>
>> function allfreq_zscores
>>
>> name = {'lex','lexmis','ster','stermis'};
>> ldir = '/analyse/12/Project0042/Gender_new/dat-files_multitaper/';
>> path = {'anaphora/','cataphora/'};
>>
>> frq = {'lo','med'};
>> pathname = {'ana','cat'};
>> %pathname = {'cat'};
>> %................. LO AND MEDIUM FREQUENCY ANALYSIS
>>
>> for p = 1:length(path)
>> for f = 1:length(frq)
>> for i = 1:length(name)
>> load(sprintf('%s%s%s_%s.mat',ldir,path{p},frq{f},name{i}));
>> for j = 1:20
>> if f == 1
>> if i == 1
>> freq = freqlo_lexmatch{j};
>> elseif i == 2
>> freq = freqlo_lexmis{j};
>> elseif i == 3
>> freq = freqlo_stermatch{j};
>> elseif i == 4
>> freq = freqlo_stermis{j};
>> end;
>> elseif f == 2
>> if i == 1
>> freq = freqmed_lexmatch{j};
>> elseif i == 2
>> freq = freqmed_lexmis{j};
>> elseif i == 3
>> freq = freqmed_stermatch{j};
>> elseif i == 4
>> freq = freqmed_stermis{j};
>> end;
>> end;
>>
>> double = struct2double(freq);
>> clear freq;
>>
>> %... check if there is the trial-dimension or not
>> if length(size(double.powspctrm)) == 4
>> double = freqdescriptives([],double);
>> end;
>>
>> cfg = [];
>> cfg.baseline = [-0.5 0];
>> cfg.baselinetype = 'zscore';
>> freq = freqbaseline(cfg,double);
>> clear double
>>
>> freqdes{j} = struct2single(freq);
>> clear freq
>> end; % subject loop
>> save(sprintf('%s%s_%s_z_
>> %s.mat',ldir,pathname{p},frq{f},name{i}),'freqdes');
>> clear freqdes
>> end; % condition loop
>> end; % frequency loop
>> end; % path loop
>>
>> %.................. HI FREQUENCY ANALYSIS
>>
>> disp('SWITCHING TO HIGH FREQUENCIES')
>>
>> for p = 1:length(path); %two different paths
>> for i = 1:length(name); %four different conditions
>> for j = 1:20 %(length of subjects)
>> tmp=load(sprintf('%s%shi_freq_%d_%d.mat',ldir,path{p},i,j));
>>
>> % convert to double before starting calculations
>> double = struct2double(tmp.single);
>> clear freq
>>
>> % average across trials using freqdescriptives
>> double = freqdescriptives([],double);
>>
>> % do baseline normalization across the AVERAGED trials (for
>> normalization
>> % over SINGLE trials, switch around freqdescriptives and
>> freqbaseline)
>> clear cfg;
>> cfg.baseline = [-0.5 0];
>> cfg.baselinetype = 'zscore';
>> fqhi = freqbaseline(cfg,double);
>> clear double
>>
>> freqdes{j} = struct2single(fqhi);
>> clear fqhi
>> end; % subject loop/ j-loop
>> %save freqdescriptives of 20 subjets (single precision) into one
>> cell-array, and save that
>> %per condition.
>> save(sprintf('%s%s_hi_z_%s.mat',ldir,pathname{p},name{i}),'freqdes');
>> clear freqdes
>> end; % condition loop / i-loop
>> end; % path loop
>> exit;
>>
>> --------------------------------------
>>
>> PLOTTING SCRIPT
>>
>> %.................HI FREQUENCY ANALYSIS PLOTS
>>
>> clear all;
>> load(sprintf('cat_hi_z_lex.mat'));
>> hi_lmatch=freqdes;
>> clear freqdes
>>
>> load(sprintf('cat_hi_z_lexmis.mat'));
>> hi_lmis=freqdes;
>> clear freqdes
>>
>> load(sprintf('cat_hi_z_ster.mat'));
>> hi_smatch=freqdes;
>> clear freqdes
>>
>> load(sprintf('cat_hi_z_stermis.mat'));
>> hi_smis=freqdes;
>> clear freqdes
>>
>>
>> clear grandhi1_lexmatch grandhi1_lmis grandhi1_smatch grandhi1_smis;
>> cfg = [];
>> grandhi1_lmatch = freqgrandaverage(cfg, hi_lmatch{:});
>> grandhi1_lmis = freqgrandaverage(cfg, hi_lmis{:});
>> grandhi1_smatch = freqgrandaverage(cfg, hi_smatch{:});
>> grandhi1_smis = freqgrandaverage(cfg, hi_smis{:});
>>
>> clear avgdif_a;
>> clear avgdif_b;
>> avgdif_a = grandhi1_lmis;
>> avgdif_a.powspctrm = ((grandhi1_lmis.powspctrm -
>> grandhi1_lmatch.powspctrm)./grandhi1_lmatch.powspctrm).*100;
>>
>> avgdif_b = grandhi1_smis;
>> avgdif_b.powspctrm = ((grandhi1_smis.powspctrm -
>> grandhi1_smatch.powspctrm)./grandhi1_smatch.powspctrm).*100;
>>
>> clear cfg;
>> load('elec.mat');
>> % scale the electrodes to a realistic head size (in cm)
>> elec.pnt = 10*elec.pnt;
>> clear cfg;
>> cfg= [];
>> cfg.elec = elec;
>> cfg.colorbar = 'yes';
>> cfg.xparam = 'time';
>> cfg.yparam = 'freq';
>> cfg.zparam = 'powspctrm';
>> cfg.showlabels = 'yes';
>> cfg.layout = 'sibylle.lay';
>> cfg.interactive = 'yes';
>> cfg.title = 'lexical_conditions';
>> cfg.xlim = ([-0.5 1.5]);
>> cfg.ylim = [30 130];
>> %cfg.zlim = [-50 50];
>> figure; multiplotTFR(cfg, avgdif_a);
>> title('FreqHi Cata: lexical match vs. mismatch');
>>
>> clear cfg;
>> cfg= [];
>> cfg.elec = elec;
>> cfg.colorbar = 'yes';
>> cfg.xparam = 'time';
>> cfg.yparam = 'freq';
>> cfg.zparam = 'powspctrm';
>> cfg.showlabels = 'yes';
>> cfg.layout = 'sibylle.lay';
>> cfg.interactive = 'yes';
>> cfg.title = 'lexical_conditions';
>> cfg.xlim = ([-0.5 1.5]);
>> cfg.ylim = [30 130];
>> %cfg.zlim = [-50 50];
>> figure; multiplotTFR(cfg, avgdif_b);
>> title('FreqHi Cata: stereotypicalmatch vs. mismatch');
>> --------------------------------
>>
>> ----------------------------------
>> 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/neuroimaging/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
> and http://www.ru.nl/neuroimaging/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 and http://www.ru.nl/neuroimaging/fieldtrip.
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