[FieldTrip] Baseline Correction using 'relchange' or 'db'
Stephen Whitmarsh
stephen.whitmarsh at gmail.com
Thu Jul 30 22:23:45 CEST 2015
Nice one Anne - let's hope so!
On 30 July 2015 at 21:44, anne Hauswald <anne.hauswald at me.com> wrote:
> Hi Mick,
>
> this might be too trivial to be the reason, but is the script below the
> actual code you run?
> Because you call the ft_freqbaseline before you set the cfg.
> The default without cfg.baseline is ’no’.
> You might not baseline-corretcing the way you think…
>
> Good luck
> Anne
>
>
> On 30.07.2015, at 16:50, mick.lehmann at uzh.ch wrote:
>
> Dear Stephen and Jim,
>
> sorry that I wasn't clear before: Before calculating the grand average, I
> applied the baseline correction in a separate script:
>
>
> TF_Remembered_db = ft_freqbaseline(cfg, TF_Remembered)
> cfg.baseline = [-1 -.1 ];
> cfg.baselinetype = 'db';
> cfg.parameter = 'powspctrm';
>
> I repeated the same procedure for the second variable (TF_NotRemembered)
> and saved them as 'TF_Remembered_db' and 'TF_NotRemembered_db'
> respectively. From then on I used only the - as I thought - baseline
> corrected variables. However, calculating the statistics on the differences
> between the two variables was different from plotting the differences. As I
> figured out, the function for plotting (ft_multiplotTFR) includes the
> following step for baseline correction:
>
> % Apply baseline correction:
> if ~strcmp(cfg.baseline, 'no')
> % keep mask-parameter if it is set
> if ~isempty(cfg.maskparameter)
> tempmask = data.(cfg.maskparameter);
> end
> data = ft_freqbaseline(cfg, data);
> % put mask-parameter back if it is set
> if ~isempty(cfg.maskparameter)
> data.(cfg.maskparameter) = tempmask;
> end
> end
>
> The post stimulus data is either corrected again or for the first time for
> pre stimulus power. The latter would make sense, since I can't find a
> similar correction step for the statistics (e.g. ft_statistics_montecarlo
> or ft_freqstatistics) and therefore the have to assume that the data is
> not baseline corrected. This assumption is further supported by the fact
> that if I don't indicate the following in the plotting script the plot is
> not baseline corrected as well:
>
> cfg.baseline = [-1 -.1];
> cfg.baselinetype = 'db';
>
>
>
> I hope very much that this information is sufficient for an external to
> understand the procedures and the resulting issue.
>
> Best regards,
> Mick
>
> -----fieldtrip-bounces at science.ru.nl schrieb: -----
> An: fieldtrip at science.ru.nl
> Von: fieldtrip-request at science.ru.nl
> Gesendet von: fieldtrip-bounces at science.ru.nl
> Datum: 30.07.2015 12:16
> Betreff: fieldtrip Digest, Vol 56, Issue 27
>
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>
> Today's Topics:
>
> 1. Re: Baseline Correction using 'relchange' or 'db'
> (mick.lehmann at uzh.ch)
> 2. Re: Baseline Correction using 'relchange' or 'db'
> (Stephen Whitmarsh)
> 3. Re: FW: align MRI- headmodel- EEG electrodes problem
> (Herring, J.D. (Jim))
> 4. Re: Baseline Correction using 'relchange' or 'db'
> (mick.lehmann at uzh.ch)
> 5. Re: Baseline Correction using 'relchange' or 'db'
> (Herring, J.D. (Jim))
> 6. Re: Baseline Correction using 'relchange' or 'db' (Eelke Spaak)
> 7. Re: Creating a New CTF Ds file (Luke Bloy)
> 8. Re: Creating a New CTF Ds file (Tom Holroyd)
> 9. Re: FW: align MRI- headmodel- EEG electrodes problem
> (Berdakh Abibullaev)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Jul 2015 12:48:47 +0200
> From: mick.lehmann at uzh.ch
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] Baseline Correction using 'relchange' or 'db'
> Message-ID:
> <OFB07CB436.0F6C069C-ONC1257E91.003B65E3-C1257E91.003B65E6 at lotus.uzh.ch>
>
>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Stephan,
>
> the whole script with the designmatrix looks as follows. It is a
> within-subject design with two conditions.?
>
> load?ga_TFCond1
> load?ga_TFCond2
> load neighbours
>
> cfg = [];
> cfg.channel ? ? ? ? ?= 'all';
> cfg.latency ? ? ? ? ?= [0 2];
> cfg.avgovertime ? ? ?= 'yes';
> cfg.frequency ? ? ? ?= [5 7];
> cfg.avgoverfreq ? ? ?= 'yes';
> cfg.method ? ? ? ? ? = 'montecarlo';?
> cfg.statistic ? ? ? ?= 'ft_statfun_depsamplesT';
> cfg.correctm ? ? ? ? = 'cluster';
> cfg.clusteralpha ? ? = 0.05;
> cfg.clusterstatistic = 'maxsum';
> cfg.minnbchan ? ? ? ?= 2;
> cfg.tail ? ? ? ? ? ? = 0;
> cfg.clustertail ? ? ?= 0;
> cfg.alpha ? ? ? ? ? ?= 0.05;
> cfg.numrandomization = 500;
> cfg.neighbours ? ? ? = neighbours;
>
>
> subj = 20;
> design = zeros(2,2*subj);
> for i = 1:subj
> ? design(1,i) = i;
> end
> for i = 1:subj
> ? design(1,subj+i) = i;
> end
> design(2,1:subj) ? ? ? ?= 1;
> design(2,subj+1:2*subj) = 2;
>
> cfg.design ? = design;
> cfg.uvar ? ? = 1;
> cfg.ivar ? ? = 2;
>
>
> stat = ft_freqstatistics(cfg, ga_TFCond1, gaTF_Cond2);
>
>
> Thanks a lot for your efforts!
>
> Kind regards,
> Mick
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> ------------------------------
>
> Message: 2
> Date: Wed, 29 Jul 2015 11:53:07 +0000
> From: Stephen Whitmarsh <stephen.whitmarsh at ki.se>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Baseline Correction using 'relchange' or 'db'
> Message-ID:
> <C2A579D858882B47926827674B07F5015844ED66 at KIMSX02.user.ki.se>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Mick,
>
> The designmatrix looks fine to me.
> I have not idea what might go wrong, but if I were you I would do the
> following checks:
>
> 1) Calculate the difference of the TFRs by subtracting the two (manually
> or with ft_math) after you did the baselinecorrection for each - i.e.
> exactly what you were giving to freqanalysis. Then plot the results using
> topoplotTFR without any baseline in the configuration of topoplotTFR. This
> should tell you whether the right stuff is going into freqstatistics.
>
> 2) First do the freqanalysis without averaging over frequencies or using
> any clustering. Then plot the t-values (of every time-frequency point)
> using ft_topoplotTFR.
>
> This should give you a good first idea whether the statistics are behaving
> as you would expect.
>
> Hope this helps,
> Stephen
>
> ________________________________
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of mick.lehmann at uzh.ch [mick.lehmann at uzh.ch]
> Sent: 29 July 2015 12:48
> To: fieldtrip at science.ru.nl
>
> Subject: Re: [FieldTrip] Baseline Correction using 'relchange' or 'db'
>
> Dear Stephan,
>
> the whole script with the designmatrix looks as follows. It is a
> within-subject design with two conditions.
>
> load ga_TFCond1
> load ga_TFCond2
> load neighbours
>
> cfg = [];
> cfg.channel = 'all';
> cfg.latency = [0 2];
> cfg.avgovertime = 'yes';
> cfg.frequency = [5 7];
> cfg.avgoverfreq = 'yes';
> cfg.method = 'montecarlo';
> cfg.statistic = 'ft_statfun_depsamplesT';
> cfg.correctm = 'cluster';
> cfg.clusteralpha = 0.05;
> cfg.clusterstatistic = 'maxsum';
> cfg.minnbchan = 2;
> cfg.tail = 0;
> cfg.clustertail = 0;
> cfg.alpha = 0.05;
> cfg.numrandomization = 500;
> cfg.neighbours = neighbours;
>
>
> subj = 20;
> design = zeros(2,2*subj);
> for i = 1:subj
> design(1,i) = i;
> end
> for i = 1:subj
> design(1,subj+i) = i;
> end
> design(2,1:subj) = 1;
> design(2,subj+1:2*subj) = 2;
>
> cfg.design = design;
> cfg.uvar = 1;
> cfg.ivar = 2;
>
>
> stat = ft_freqstatistics(cfg, ga_TFCond1, gaTF_Cond2);
>
>
> Thanks a lot for your efforts!
>
> Kind regards,
> Mick
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> ------------------------------
>
> Message: 3
> Date: Wed, 29 Jul 2015 13:27:01 +0000
> From: "Herring, J.D. (Jim)" <j.herring at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] FW: align MRI- headmodel- EEG electrodes
> problem
> Message-ID:
> <3D00B7615FB58D46A0B49B9AD67A33EB51370F at exprd01.hosting.ru.nl>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Nadia,
>
> Looking at your images the registration seems to be quite fine. Having
> some electrodes in/outside of the head due to the issues JM addressed is
> not a problem as electrode positions are projected onto the scalp surface
> anyway when creating the leadfield.
>
> Best,
>
> Jim
>
> From: fieldtrip-bounces at science.ru.nl [
> mailto:fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl>]
> On Behalf Of Konstantina Kalogianni
> Sent: woensdag 22 juli 2015 15:53
> To: FieldTrip discussion list
> Subject: [FieldTrip] FW: align MRI- headmodel- EEG electrodes problem
>
> Hi Jan-Mathijs,
>
> You can download my best result from this link:
> https://surfdrive.surf.nl/files/public.php?service=files&t=6d591406015bcb7715ffaebd18fd7d03
> I don't think is optimal.
> Some of the frontal electrodes are placed inside the head and some of the
> back ones are floating.
>
> In my case the automatic alignment with the fiducials didn't work well, do
> you have any suggestions on how to make this in a better way?
>
> After reading posts on the discussion list, I defined left ear as what
> seems the right ear.
> But are there some other tricks that I should apply on the fiducials
> identification or at the ft_warp_apply?
>
> I agree that it will never be optimal because of the issues you described.
> But I was wondering when is it satisfying in order not to influence my
> inverse solution.
>
> One more question, is there a function that I should I use that will
> optimize my electrodes locations after doing the alignment?
>
> Thank you for your help.
>
> Best,
> Nadia
>
>
>
> From: fieldtrip-bounces at science.ru.nl<
> mailto:fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl>>
> [mailto:fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl>]
> On Behalf Of Schoffelen, J.M. (Jan Mathijs)
> Sent: dinsdag 21 juli 2015 20:55
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] align MRI- headmodel- EEG electrodes problem
>
> Hi Nadia,
>
> >From the code I cannot see any obvious flaws, but it's hard to tell,
> without some pictorial feedback. It could be that all went well, but that
> the end result is just the best that can be achieved. Note that there will
> always be some discrepancy between the head surface reconstructed from the
> anatomical image (image distortion, thresholding issues etc), and the
> electrode positions (having the cap in between, some slight inacurracy
> between the recorded fiducial positions, and the positions obtained by
> clicking in the MR-image). Do you have an image of your 'best result'?
>
> Best,
> Jan-Mathijs
>
>
> Jan-Mathijs Schoffelen, MD PhD, Senior researcher
>
> Max Planck Institute for Psycholinguistics
> Donders Centre for Cognitive Neuroimaging
>
> E-mail: j.schoffelen at donders.ru.nl<mailto:j.schoffelen at donders.ru.nl
> <j.schoffelen at donders.ru.nl>>
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
> http://www.fieldtriptoolbox.org
>
>
>
>
>
>
> On Jul 21, 2015, at 4:56 PM, Konstantina Kalogianni <
> K.Kalogianni at tudelft.nl<mailto:K.Kalogianni at tudelft.nl
> <K.Kalogianni at tudelft.nl>>> wrote:
>
> Dear fieldtrippers,
>
> I am struggling with aligning the individual MRI, the headmodel and
> electrode positions(EEG) for some days now, without any success.
> I would appreciate some help.
>
> To begin with, as an input I have the subject specific MRI which was
> segmented with the use of freesurfer and MNE software.
> I load first the MRI ,the triangulated meshes for brain skull and skin,
> and the electrodes positions of 65-channel EEG.
> I am then computing the bem headmodel from the brain skull skin (computed
> with the use of MNE software)
> Afterwards I am aligning the MRI to my headmodel (ft_volumerealign) and
> then I identify the fiducials with the interactive mode (ft_volumerealign).
> I do the transformation of the fiducial points with ft_warp_apply to the
> coordinates specified at the alignment.
> Then I call the ft_electroderealign to align my electrodes to the mri's
> fiducial points.
> And then I realign my electrodes manually.
>
> The problem is that no matter how much rotation translation scaling I do,
> it's IMPOSSIBLE TO FIT THE ELECTRODES TO THE HEADMODEL!
> I tried the volume_realign with ctf coordinates as well and I tried the
> ft_electroderalign with the interactive mode only(without matching the
> fiducials), it doesn't work.
>
> Below you can find the code that I used.
> Any ideas on this issue would be of great help!
>
>
> %% READ
> % read mri
> mri=ft_read_mri([freesurferDir 'mri\orig.mgz']);
> mri.coordsys='neuromag';
>
> % read surfaces
>
> brain=ft_read_headshape([freesurferDir
> 'bem\brain.surf\Pilot08_brain_surface']);
>
> skull=ft_read_headshape([freesurferDir
> 'bem\brain.surf\Pilot08_inner_skull_surface' ]);
> skin=ft_read_headshape([freesurferDir
> 'bem\brain.surfilot08_outer_skin_surface' ]);
>
> % read electrodes positions
> elec_file=[datadir '\raw\M10.elc'];
> elec=ft_read_sens(elec_file );
> elec.coordsys='neuromag';
> elec.label=upper(elec.label);
>
> %% HEADMODEL
> %assign values of segmented surfaces
> geom(1).tri=brain.tri;
> geom(2).tri=skull.tri;
> geom(3).tri=skin.tri;
>
> geom(1).pnt=brain.pnt;
> geom(2).pnt=skull.pnt;
> geom(3).pnt=skin.pnt;
> % compute headmodel
> vol=ft_headmodel_bemcp(geom);
> vol=ft_convert_units(vol, 'mm');
> vol.coordsys='neuromag';
>
> %% ALIGNMENTS
> %align mri and headshape
> mri_coord=ft_determine_coordsys(mri, 'interactive', 'yes');
> vol_coord=ft_determine_coordsys(vol, 'interactive', 'yes');
>
> cfg=[];
> cfg.method = 'headshape';
> cfg.headshape=vol_coord.bnd(3);
> mri_headshape=ft_volumerealign(cfg,mri_coord);
>
> %find fiducials
> cfg=[];
> cfg.method='interactive';
> cfg.coordsys='neuromag';
> mri_fid=ft_volumerealign(cfg,mri_headshape);
>
>
> %% APPLY TRANSFORMATIONS ON FIDUCIALS
>
> transm=mri_fid.transform;
> nas=ft_warp_apply(transm,mri_fid.cfg.fiducial.nas, 'homogenous');
> lpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.rpa, 'homogenous');
> rpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.lpa, 'homogenous');
>
>
>
> fid.chanpos = [nas; rpa; lpa];
> fid.elecpos =fid.chanpos;
> fid.label = {'NASION', 'RIGHTEAR','LEFTEAR'}; % same labels as in
> elec
> fid.unit = 'mm'; % same units as mri
> % Automatic electrode alignment using the fiducials
> cfg = [];
> cfg.method = 'fiducial';
> cfg.template = fid;
> cfg.elec = elec;
> cfg.fiducial = {'NASION', 'RIGHTEAR','LEFTEAR'}; % labels of
> fiducials in fid and in sens
> cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape
> elec_aligned_fid = ft_electroderealign(cfg);
>
>
> %% Interactive alignment of electrodes to fix some misalignment
>
> cfg=[];
> cfg.method='interactive';
> cfg.elec=elec_aligned_fid;
> cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape
> elec_aligned=ft_electroderealign(cfg);
>
>
>
> Best Regards,
>
> K. (Nadia) Kalogianni
> PhD candidate
>
> TU Delft /Department of Biomechanical Engneering
> Neuromuscular Control Laboratory
>
> Mekelweg 2
> 2628 CD Delft
> Room: F-1-320
> T +31 15-27 84230
> E k.kalogianni at tudelft.nl<mailto:k.kalogianni at tudelft.nl
> <k.kalogianni at tudelft.nl>>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl
> <fieldtrip at donders.ru.nl>>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 29 Jul 2015 15:55:38 +0200
> From: mick.lehmann at uzh.ch
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] Baseline Correction using 'relchange' or 'db'
> Message-ID:
> <OF712C6BF3.82EA65A9-ONC1257E91.004C2CEF-C1257E91.004C8128 at lotus.uzh.ch>
>
>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Fieltrippers,
>
> yesterday I addressed this mailing list with an issue regarding the
> baseline correction for time frequency analysis. While plotting a
> comparison of two conditions revealed exactly the results I've expected,
> the statistic didn't at all. Regardless of electrode, time window and freq
> range, the comparison of the two conditions was significantly different
> (with t-values between 8 and 10 and p < 0.001). Digging a little deeper,
> the main difference between the script for plotting and the one for stat
> analysis is that in for the figure, I've to indicate again the
> baselinewindow and the baselinetype:
>
>
> diff = gaTF_Cond1;
> diff.powspctrm = (gaTF_Cond1.powspctrm -?gaTF_Cond2.powspctrm);
>
>
> cfg = [];
> cfg.baseline ? ? = [-1 -.1];
> cfg.baselinetype = 'db'; ?
> cfg.maskstyle ? ?= 'saturation';
>
> cfg.zlim ? ? ? ? = [-3 3];
> cfg.ylim ? ? ? ? = [2 25]; ??
> cfg.xlim ? ? ? ? = [-1 2];?
> cfg.channel ? ? ? = {'all'};
> cfg.layout =
> 'C:\Users\MickLehmann\Documents\Emo_React_EEG\FieldTrip\Scripts\egi128_GSN_HydroCel3.sfp';
> cfg.interactive = 'yes'
> ft_multiplotTFR(cfg,diff);?
>
> Runningit like this, the figure looks fine. However, if I switch off the
> bold part, the figure is dark red (as the stat analysis would suggest).?
>
> In the statistic script, I don't indicate the baseline again and I've no
> clue how to implement it. Do you think that could be the problem and has
> anybody a suggestion how to address the problem??
>
> If that is actually the main issue then I'm hardly the first encountering
> this problem.
>
> Kind regards,
> Mick
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> ------------------------------
>
> Message: 5
> Date: Wed, 29 Jul 2015 14:10:02 +0000
> From: "Herring, J.D. (Jim)" <j.herring at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Baseline Correction using 'relchange' or 'db'
> Message-ID: <873A3AC5-23E9-4764-8760-095324D27832 at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Mick,
>
> Indeed, if you apply a baseline correction only while plotting the the TFR
> it could be that you get different results when running statistics on the
> non-baseline corrected data.
>
> You can apply a baseline correction on your data prior to running the
> statistical analysis by using ft_freqbaseline to your ?diff? structure with
> cfg.baseline and cfg.baselinetype having the same values as you used while
> plotting.
>
> Best,
>
> Jim
>
>
>
> On 29 Jul 2015, at 15:55, mick.lehmann at uzh.ch<mailto:mick.lehmann at uzh.ch
> <mick.lehmann at uzh.ch>> wrote:
>
> Dear Fieltrippers,
>
> yesterday I addressed this mailing list with an issue regarding the
> baseline correction for time frequency analysis. While plotting a
> comparison of two conditions revealed exactly the results I've expected,
> the statistic didn't at all. Regardless of electrode, time window and freq
> range, the comparison of the two conditions was significantly different
> (with t-values between 8 and 10 and p < 0.001). Digging a little deeper,
> the main difference between the script for plotting and the one for stat
> analysis is that in for the figure, I've to indicate again the
> baselinewindow and the baselinetype:
>
>
> diff = gaTF_Cond1;
> diff.powspctrm = (gaTF_Cond1.powspctrm - gaTF_Cond2.powspctrm);
>
>
> cfg = [];
> cfg.baseline = [-1 -.1];
> cfg.baselinetype = 'db';
> cfg.maskstyle = 'saturation';
> cfg.zlim = [-3 3];
> cfg.ylim = [2 25];
> cfg.xlim = [-1 2];
> cfg.channel = {'all'};
> cfg.layout =
> 'C:\Users\MickLehmann\Documents\Emo_React_EEG\FieldTrip\Scripts\egi128_GSN_HydroCel3.sfp';
> cfg.interactive = 'yes'
> ft_multiplotTFR(cfg,diff);
>
> Runningit like this, the figure looks fine. However, if I switch off the
> bold part, the figure is dark red (as the stat analysis would suggest).
>
> In the statistic script, I don't indicate the baseline again and I've no
> clue how to implement it. Do you think that could be the problem and has
> anybody a suggestion how to address the problem?
>
> If that is actually the main issue then I'm hardly the first encountering
> this problem.
>
> Kind regards,
> Mick
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl
> <fieldtrip at donders.ru.nl>>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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> ------------------------------
>
> Message: 6
> Date: Wed, 29 Jul 2015 15:11:52 +0100
> From: Eelke Spaak <eelke.spaak at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Baseline Correction using 'relchange' or 'db'
> Message-ID:
> <CABPNLUoxbiy5Rx=HiUkN29ovG12nnGcEoLZszafQh7chf2OyYA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Mick,
>
> If you want to run statistics on baseline-corrected time-frequency
> data, you should apply ft_freqbaseline on your data before entering it
> into ft_freqstatistics. Let us know if that solves the problem.
>
> Best,
> Eelke
>
> On 29 July 2015 at 14:55, mick.lehmann at uzh.ch <mick.lehmann at uzh.ch> wrote:
> > Dear Fieltrippers,
> >
> > yesterday I addressed this mailing list with an issue regarding the
> baseline
> > correction for time frequency analysis. While plotting a comparison of
> two
> > conditions revealed exactly the results I've expected, the statistic
> didn't
> > at all. Regardless of electrode, time window and freq range, the
> comparison
> > of the two conditions was significantly different (with t-values between
> 8
> > and 10 and p < 0.001). Digging a little deeper, the main difference
> between
> > the script for plotting and the one for stat analysis is that in for the
> > figure, I've to indicate again the baselinewindow and the baselinetype:
> >
> >
> > diff = gaTF_Cond1;
> > diff.powspctrm = (gaTF_Cond1.powspctrm - gaTF_Cond2.powspctrm);
> >
> >
> > cfg = [];
> > cfg.baseline = [-1 -.1];
> > cfg.baselinetype = 'db';
> > cfg.maskstyle = 'saturation';
> > cfg.zlim = [-3 3];
> > cfg.ylim = [2 25];
> > cfg.xlim = [-1 2];
> > cfg.channel = {'all'};
> > cfg.layout =
> >
> 'C:\Users\MickLehmann\Documents\Emo_React_EEG\FieldTrip\Scripts\egi128_GSN_HydroCel3.sfp';
> > cfg.interactive = 'yes'
> > ft_multiplotTFR(cfg,diff);
> >
> > Runningit like this, the figure looks fine. However, if I switch off the
> > bold part, the figure is dark red (as the stat analysis would suggest).
> >
> > In the statistic script, I don't indicate the baseline again and I've no
> > clue how to implement it. Do you think that could be the problem and has
> > anybody a suggestion how to address the problem?
> >
> > If that is actually the main issue then I'm hardly the first encountering
> > this problem.
> >
> > Kind regards,
> > Mick
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 29 Jul 2015 15:12:59 +0000
> From: Luke Bloy <luke.bloy at gmail.com>
> To: Tom Holroyd <tomh at kurage.nimh.nih.gov>
> Cc: FieldTrip list serve <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Creating a New CTF Ds file
> Message-ID:
> <CAG5Ru-rsmdr3okSjnAxqwp8RO_XXSTi8pa_1iVJCXtS=6=PpVA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thanks for the replies.
>
> Jan-Mathijs, I am working on some preprocessing/artifact correction
> projects and would like the option to write back to the DS format so that
> others in my lab, using native ctf tools or besa, can easily incorporate
> what I am doing into their pipelines. Starting with readCTFds.m and the
> files in external/ctf is probbaly a good idea. Thanks.
>
> Tom, rewriting the meg4 file would certainly work for what I need to do.
> Would you be willing to share an example (Python would be fine) of writing
> out to the meg4 file.
>
> Best,
> Luke
>
> On Tue, 28 Jul 2015 at 16:12 Tom Holroyd <tomh at kurage.nimh.nih.gov> wrote:
>
> > On Tue, 28 Jul 2015 17:03:41 +0000
> > Luke Bloy <luke.bloy at gmail.com> wrote:
> >
> > > Is anyone aware of any tools for writing CTF DS files out from
> > > fieldtrip data structures?
> >
> > Well, I have Python code. But the usual way to go here is to use an
> > existing dataset. The CTF .meg4 file is a "flat" file*, so you can read
> > in a CTF dataset, modify the data, and then easily re-write only
> > the .meg4 file without changing any of the other files, assuming the
> > modification doesn't change the trial structure or length of data.
> >
> > The only thing you need to do is convert the internal floating point
> > representation (units of Tesla) back into the .meg4 file representation
> > (32-bit integers) by inverting the gain calculation, using the same
> > gains stored in the header.
> >
> > With some trickery, you can even make shorter datasets from existing
> > ones using the usual newDs tool, and then rewrite the short .meg4 file
> > with whatever data. Writing CTF datasets from scratch is certainly
> > possible, but you're still going to be copying things from existing
> > datasets (such as sensor geometry and gain factors).
> >
> > * with an 8 byte (constant) header
> >
> > --
> > Dr. Tom
> > --
> > "There are not more than five musical notes,
> > yet the combinations of these five give rise to
> > more melodies than can ever be heard." -- Sun Tzu
> >
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> ------------------------------
>
> Message: 8
> Date: Wed, 29 Jul 2015 12:12:05 -0400
> From: Tom Holroyd <tomh at kurage.nimh.nih.gov>
> To: Luke Bloy <luke.bloy at gmail.com>
> Cc: FieldTrip list serve <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Creating a New CTF Ds file
> Message-ID: <20150729121205.7ec413af at kurage.nimh.nih.gov>
> Content-Type: text/plain; charset=US-ASCII
>
> On Wed, 29 Jul 2015 15:12:59 +0000
> Luke Bloy <luke.bloy at gmail.com> wrote:
>
> > Tom, rewriting the meg4 file would certainly work for what I need to
> > do. Would you be willing to share an example (Python would be fine)
> > of writing out to the meg4 file.
>
> Here's a snippet. If you are reading it with Matlab, the important
> thing you'll need is the array of channel gains. I don't know where
> Fieldtrip stashes those, but they are there somewhere.
>
> # Get the channel gains. There are three sets of gains in the
> # res4 file, and they are just multiplied together to get one
> # gain for each of the M channels.
>
> gain = zeros(M)
> for m in range(M):
> sr = res4.sensRes[m][0]
> gain[m] = sr[sr_properGain] * sr[sr_qGain] * sr[sr_ioGain]
>
> # Format to write big endian 32-bit integers. CTF .meg4 files
> # are big endian 32-bit ints. Here, newlen is the length of
> # a trial in samples.
>
> be_int = Struct(">%di" % newlen)
>
> # Open the file and write the header.
>
> meg4name = os.path.join(newdsname, newset + ".meg4")
> f = open(meg4name, "w")
> f.write("MEG41CP\x00")
>
> # This loop only writes one trial. If there's more than
> # one, the next trial just goes right after the first one.
> # Within a trial it's channels by samples.
>
> for m in range(M):
> #print "channel", res4.chanName[m]
>
> # Get the data to write into trialbuf, in Tesla.
> trialbuf[] = ...
>
> # convert to int and write
> trialbuf *= gain[m]
> l = map(int, trialbuf + .5) # round to nearest int
> f.write(be_int.pack(*l)) # writes newlen ints
>
> f.close()
>
> If the mailer screws up the formatting, just let me know
> and I can send you this whole app, which is dsimDs, which
> creates simulated MEG data from dipoles and noise. This is
> easy enough to convert to Matlab, anyway, once you know
> where the gains are (I'm not an expert in Matlab so I don't
> know how to write files ...)
>
> --
> Dr. Tom
> --
> "There are not more than five musical notes,
> yet the combinations of these five give rise to
> more melodies than can ever be heard." -- Sun Tzu
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 29 Jul 2015 11:50:14 -0500
> From: Berdakh Abibullaev <berdakho at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] FW: align MRI- headmodel- EEG electrodes
> problem
> Message-ID:
> <CAOjxBaqkG=oah_yVQjQyFrvhabAU6+18Cb6FUjPM5X7UkKLS+Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> ?You could use the following function to project the electrodes onto the
> head surface, right after calling ft_electroderealign.
>
> [vol, elec] = ft_prepare_vol_sens(volume, electrode_aligned)?
>
> As Jim mentioned this function seems to be called internally while
> computing the leadfield.
>
> Best,
> Berdakh.
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