[FieldTrip] combining magnetometers and planad gradiometers for analysis
jan-mathijs schoffelen
jan.schoffelen at donders.ru.nl
Fri Jun 3 15:22:10 CEST 2011
Dear Stephan,
Ah, you're right. I forgot about the mne2grad... Sorry.
Regarding the SSP vectors I forgot to mention that of course the
sensor data needs to have the SSP vectors incorporated as well, if
such info is to be applied to the leadfields too? Either the data on
disk is already balanced, or the coefficients need to be applied after
reading in the unbalanced data. I don't know enough about the elekta-
software/mne-software to know what is happening to the data when the
ssp vectors are computed, but once we know enough details it should be
straightforward to build it into fieldtrip.
Best,
JM
On Jun 3, 2011, at 3:08 PM, Stephan Moratti wrote:
> Hi Jan-Mathijs,
>
> I had just a look at fif2grad.m and it seems to me that the
> information of hdr.orig.projs is not used to construct the .tra
> field. It only codes for magnetometers 1 and for the two
> gradiometers 1 and -1 (to get the difference). Going through the
> code I found out that FT uses mne2grad.m rather than fif2grad.m. But
> mne2grad.m does not use the info in hdr.orig.projs. Thus, it seems
> the information does not go into grad.tra. (So I guess the
> topographies and leadfields will not be correct when SSP vectors are
> used).
>
> Best,
>
> Stephan
>
> El 03/06/2011, a las 13:11, jan-mathijs schoffelen escribió:
>
>> Hi Stephan et al,
>>
>> Any balancing coefficients (e.g. the digital weights for the bti-
>> system, or ctf's 3d order gradient coefficients) are only applied
>> to the leadfield if they end up in the data.grad.tra matrix.
>> These .tra matrices will be compiled when reading the data header,
>> by functions like XXX2grad (in fileio/private: ctf2grad, bti2grad,
>> fif2grad).
>> You can check whether it is constructed using hdr.orig.projs.
>> If not, it may be worthwile to implement I guess.
>>
>> Best,
>>
>> JM
>>
>>
>>
>> On Jun 3, 2011, at 11:00 AM, Stephan Moratti wrote:
>>
>>> Hi Michael y Elena,
>>>
>>> I am following your discussion with great interest as I have just
>>> started to work with Neuromag data. As FT uses the MNE toolbox to
>>> read the data I assume that the SSP vectors are applied to the
>>> data during reading the data. However, the SSP vectors are stored
>>> in "data.hdr.orig.projs". However, when I go on with averaging in
>>> the ERF from timelockanalysis I cannot find this info. So my
>>> question is, does FT apply the SSP vectors later on also to the
>>> leadfield when calculating it? I assume that not, as the SSP
>>> vectors are not passed on further. How can I apply the SSP vectors
>>> to the leadfield to get correct results?
>>>
>>> Best and thanks,
>>>
>>> STephan
>>>
>>> El 02/06/2011, a las 19:20, Michael Wibral escribió:
>>>
>>>> Hi Elena,
>>>>
>>>> I assume that you were well aware of the difficulties in
>>>> beamforming evoked activty and baseline normalisation and these
>>>> things, your results really look that way. I mus say I am quite
>>>> puzzled by the results - could it be a color scaling problem in
>>>> the plot? I think this mmay be a problem because most of your
>>>> plot is a peak power, only a tiny corner seems to be in a low-
>>>> amplitude range.
>>>>
>>>> What you could do as a workaround is to average the separate
>>>> results with a weighting per voxel and that is corresponding to
>>>> the squared norms of the leadfields for the respective modalities
>>>> for a given voxel , this would guarantee equal amounts of
>>>> backprojected noise from both modalities (if I'm not mistaken).
>>>>
>>>> Michael
>>>> PS: I am away for a couple of days, but after that, I'll be happy
>>>> to resume this discussion.
>>>>
>>>>
>>>> Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
>>>> Gesendet: Jun 2, 2011 6:22:03 PM
>>>> An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl
>>>> >
>>>> Betreff: Re: [FieldTrip] combining magnetometers and planad
>>>> gradiometers for analysis
>>>>
>>>> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face
>>>> { font-family: "Cambria Math"; }@font-face { font-family:
>>>> "Calibri"; }@font-face { font-family: "Cambria"; }p.MsoNormal,
>>>> li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-
>>>> size: 12pt; font-family: Cambria; }.MsoChpDefault { font-family:
>>>> Cambria; }div.WordSection1 { page: WordSection1; }
>>>> Dear Michael,
>>>>
>>>>
>>>> I have tried to multiply the leadfield by -1 as you suggested:
>>>>
>>>>
>>>> for i = 1 : size (grid.leadfield, 2)
>>>>
>>>> grid.leadfield{i}(3:3:306, :) = -1*grid.leadfield{i}
>>>> (3:3:306, :);
>>>>
>>>> end
>>>>
>>>>
>>>> This had no effect on the 'lcmv' output. I attached the pictures
>>>> for ‘GRA only, ’MAG only’ and ‘GRA + MAG’
>>>>
>>>>
>>>> In this experiment I measured evoked field in response to the
>>>> unilateral (left) click.
>>>>
>>>> The source is expected to be in the right superior temporal
>>>> cortex. This is the case for ‘GRA only' and ’MAG only’
>>>> datasets. The combined sensors give meaningless result.
>>>>
>>>>
>>>> Elena
>>>>
>>>>
>>>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl
>>>> ] on behalf of Michael Wibral [michael.wibral at web.de]
>>>> Sent: Wednesday, June 01, 2011 4:04 PM
>>>> To: Email discussion list for the FieldTrip project
>>>> Subject: Re: [FieldTrip] combining magnetometers and planad
>>>> gradiometers for analysis
>>>>
>>>>
>>>> Dear Elena,
>>>>
>>>> could you give the following a try: invert (*-1) the leadfileds
>>>> for one of the two sensor types. Let me know what happens.
>>>> I would also be interested in taking a look at the results -
>>>> maybe you could sent images off-list: Michael.Wibral <at> web.de.
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>> Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
>>>> Gesendet: Jun 1, 2011 12:23:29 PM
>>>> An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
>>>> Betreff: [FieldTrip] combining magnetometers and planad
>>>> gradiometers for analysis
>>>>
>>>> @font-face { font-family: "Arial"; }@font-face { font-family:
>>>> "Times"; }@font-face { font-family: "\FF2D \FF33 \660E \671D
>>>> "; }@font-face { font-family: "Cambria Math"; }@font-face { font-
>>>> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal
>>>> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family:
>>>> Cambria; }p { margin-right: 0cm; margin-left: 0cm; font-size:
>>>> 10pt; font-family: Times; }.MsoChpDefault { font-family:
>>>> Cambria; }div.WordSection1 { page: WordSection1; }
>>>> Dear fieldtrippers,
>>>>
>>>> This message is mainly for Neuromag users.
>>>>
>>>>
>>>> When I do 'lcmv' beamforming analysis separately on planar
>>>> gradiometers or magnetometers, I get quite meaningful results.
>>>>
>>>> If I combine the two types of sensors without weighting, the
>>>> result is meaningless.
>>>>
>>>> Apparently, the algorithm does not take care of different scales
>>>> and units of the GRA and MAG measurements. Does anybody know how
>>>> to deal with this problem?
>>>>
>>>>
>>>>
>>>> Elena
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> ________________________________________________________
>>> Stephan Moratti, PhD
>>>
>>> see also: http://web.me.com/smoratti/
>>>
>>> Universidad Complutense de Madrid
>>> Facultad de Psicología
>>> Departamento de Psicología Básica I
>>> Campus de Somosaguas
>>> 28223 Pozuelo de Alarcón (Madrid)
>>> Spain
>>>
>>> and
>>>
>>> Center for Biomedical Technology
>>> Laboratory for Cognitive and Computational Neuroscience
>>> Parque Científico y Tecnológico de la Universidad Politecnica de
>>> Madrid
>>> Campus Montegancedo
>>> 28223 Pozuelo de Alarcón (Madrid)
>>> Spain
>>>
>>>
>>> email: smoratti at psi.ucm.es
>>> Tel.: +34 679219982
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de
> Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.: +34 679219982
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110603/f64ec0e4/attachment-0001.html>
More information about the fieldtrip
mailing list