[FieldTrip] Estimate coherence between conditions?
Maria Hakonen
maria.hakonen at gmail.com
Mon Jul 10 14:37:20 CEST 2017
Hi Maité,
Many thanks for your answer!
I have now tried to get coherence between two conditions following the
Appendix 1 (I have also used the same data as in Appendix 1;
http://www.fieldtriptoolbox.org/tutorial/coherence).
As far as I understand, I should first calculate ft_freqanalysis and
ft_sourceanalysis separately for condition 1 and condition 2 as follows:
*Condition 1:*
Compute the cross-spectral density matrix for 18 Hz:
cfg = [];
cfg.method = 'mtmfft';
cfg.output = 'powandcsd';
cfg.foilim = [18 18];
cfg.tapsmofrq = 5;
cfg.keeptrials = 'yes';
freq1 = ft_freqanalysis(cfg, data);
The Appendix 1 also defines:
cfg.channelcmb = {'MEG' 'MEG';'MEG' 'EMGlft'};
However, I think that in my case channelcmb is not needed since default =
{'all' 'all'}.
Thereafter, I used ft_sourceanalysis as follows:
cfg = [];
cfg.method = 'dics';
cfg.frequency = 18;
cfg.hdmfile = 'SubjectCMC.hdm';
cfg.inwardshift = 1;
cfg.grid.resolution = 1;
cfg.grid.unit = 'cm';
source1 = ft_sourceanalysis(cfg, freq);
(The Appendix 1 also defines: cfg.refchan = 'EMGlft';)
*Condition 2:*
I calculated cross-spectral density exactly in the same way as in condition
1 but used data from condition 2.
In ft_sourceanalysis, I set keepfilter and keepleadfiled as “yes”:
cfg = [];
cfg.method = 'dics';
cfg.frequency = 18;
cfg.hdmfile = 'SubjectCMC.hdm';
cfg.inwardshift = 1;
cfg.grid.resolution = 1;
cfg.grid.unit = 'cm';
cfg.keepfilter = ‘yes’;
cfg.keepleadfield = ‘yes’;
source2 = ft_sourceanalysis(cfg, freq2);
Thereafter, I selected a source that in inside the brain from source2 and
included it’s position, leadfield and filter in refdip:
refdip =
pos: [5 -5 -1]
leadfield: {[151x3 double]}
filetr: [3x151 double]
After this, I run ft_sourceanalysis:
cfg = [];
cfg.method = 'dics';
cfg.frequency = 18;
cfg.hdmfile = 'SubjectCMC.hdm';
cfg.inwardshift = 1;
cfg.grid.resolution = 1;
cfg.grid.unit = 'cm';
cfg.refdip = refdip;
source = ft_sourceanalysis(cfg, freq1);
Here, I used cross spectral density matrix computed from condition 1 (i.e.
freq1). I am not sure, whether I should also somehow take into account the
data from condition 2 when calculating freq?
Appendix 1 uses EMGlft as refchan in ft_sourceanalysis and has defined
cfg.channelcmb = {'MEG' 'MEG';'MEG' 'EMGlft'}; in ft_freqanalysis.
The coherence in the position of the reference dipole (i.e. 5 -5 -1) seems
to be one, as would be expected since I used the same data in both
conditions.
Best,
Maria
2017-07-07 9:08 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:
> Hi Maria,
>
> I think there is more than one solution for what you are aiming to do.
> Maybe a more experienced user or developer could show you the most
> straightforward way (?).
>
> IMO, using LCMV is more direct for this application because with DICS you
> will need to provide the reference signal (i.e., the source timecourse from
> the other condition). Therefore, you will need to apply LCMV anyway.
>
> You could apply a band-pass filter to the channel activity before
> localizing the frequency band of interest with LCMV. Alternatively, you
> could obtain the virtual channels (without band pass) and define the
> frequency bands of interest when computing the coherence as in the tutorial
> (see ft_freqanalysis steps at http://www.fieldtriptoolbox.
> org/tutorial/coherence#computing_the_coherence).
> With DICS, in this case, I see it more intricate: 1) obtain the source
> timecourses of condition 2 with LCVM; 2) compute the cross spectral density
> between all data channels and each source timecourse (reference signal); 3)
> compute DICS for each reference signal. Of course, you don't need to
> compute the coherence for the whole brain, but only for the source of
> interest. For each reference signal, you could change the cfg.grid.inside
> value to include only the position of the voxel of interest (the same voxel
> of the reference signal).
> I hope this helps.
>
> Best,Maité
>
> Hi Maité,
>
> Many thanks for your advice again!
>
> I have been wondering whether I could calculate coherence straight from
> the cross spectros without reference signals or virtual channels by using
> beamformer_dics. In beamformer_dics, it seems to be possible to define the
> location of the dipole with which coherence is computed (i.e. refdip).
> However, I am not sure if it is possible to calculate the coherence between
> the same brain region in two different conditions.
>
> Best,
> Maria
>
> 2017-06-29 12:57 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:
>
>> Hi Maria,
>> for obtaining the sources timecourses (aka virtual channels) you can follow the tutorials pasted below.
>>
>> Best,Maité
>> http://www.fieldtriptoolbox.org/tutorial/connectivity#extract_the_virtual_channel_time-series
>> http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors#extract_the_virtual_channel_time-series
>>
>> Hi Maité,
>>
>> Thank for your answer again!
>>
>> However, I would need to calculate coherence within certain frequency bands and, therefore, I would like to use dics. The examples in the links seem to use lcmv. Could you please let me know how I can get coherence between conditions using dics?
>>
>> Best,
>>
>> Maria
>>
>>
>> 2017-06-26 12:45 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:
>>
>>> Hi Maria,
>>> maybe in this case it is better that you export the sources timecourses, build a data matrix with them and treat them in the same way as you did with the channels.
>>>
>>> Best,Maité
>>>
>>>
>>> Hi Maité,
>>>
>>> Could you please yet let me know how to get the sources timecources?
>>> source = ft_sourceanalysis(cfg, freq); only gives
>>> source =
>>>
>>> freq: 18
>>> cumtapcnt: [180x1 double]
>>> dim: [19 15 15]
>>> inside: [4275x1 logical]
>>> pos: [4275x3 double]
>>> method: 'average'
>>> avg: [1x1 struct]
>>> cfg: [1x1 struct]
>>>
>>> Best,
>>> Maria
>>>
>>> 2017-06-25 13:53 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:
>>>
>>>> Hi Maité,
>>>>
>>>> Thank you for your answer!
>>>>
>>>> I have managed to calculate the coherence between two conditions in the sensor space in the way you suggested. However, I haven't managed to calculate the coherence between conditions in the source space (i.e. Appendix 1 in http://www.fieldtriptoolbox.org/tutorial/coherence). ft_sourceanalysis doesn't have channelcmb. I wonder if anyone has any solutions for this?
>>>>
>>>> BTW. I didn't get the answer to my question in my email but found it from Fieldtrip archive. However, I have also got some other emails from fieldtrip discussion forum.
>>>>
>>>> Best,
>>>>
>>>> Maria
>>>>
>>>>
>>>> Hi Maria,
>>>> Here it is a possible solution. First, rename channels from one of both conditions: for example, for condition 2, {'ch01cond2', 'ch02cond2', ...}. Then, append the data from both conditions. In ft_freqanalysis introduce all the channels combinations you want:
>>>>
>>>> cfg.channel = {'MEG' 'ch01cond2' 'ch02cond2' ...};
>>>> cfg.channelcmb = {'ch01' 'ch01cond2'; 'ch02' 'ch02cond2'};
>>>> As I understand, you could use the same channelcmb later on in ft_connectivityanalysis.
>>>> I hope it helps.
>>>> Best wishes,Maité
>>>>
>>>>
>>>>
>>>> Dear FieldTrip experts,
>>>>
>>>> I have just started to use Fieldtrip and would like to estimate
>>>> coherence between MEG responses measured in two different conditions from
>>>> the same cortical areas. The example in Appendix 1 is close to what I would
>>>> like to do:
>>>> http://www.fieldtriptoolbox.org/tutorial/coherence
>>>>
>>>> However, in the example, coherence is calculated between the reference
>>>> signal (EMG) and all MEG channels. Could it be possible to calculate
>>>> coherence between each MEG channel in one condition and the same MEG
>>>> channels in the other condition, that is:
>>>> ch1 in cond1 vs. ch1 in cond2, ch2 in cond1 vs. ch2 in cond2, ...
>>>>
>>>> As far as I understand, the example in Appendix 1 would do this:
>>>> ch1 in cond1 vs. all channels in cond2, ch2 in cond ch1 all channels in
>>>> cond2, ...
>>>>
>>>> Best,
>>>> Maria
>>>>
>>>>
>>>
>>
>
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