[FieldTrip] Lead Field Units in LCMV Beamformer
Schoffelen, J.M. (Jan Mathijs)
janmathijs.schoffelen at donders.ru.nl
Mon May 2 09:36:43 CEST 2022
When you state that the scale is ‘much too large’ that suggests that you have a specific expectation of the values that you typically get (using other software? what is the unit convention in that software?). Since you are not clear on what type of MEG system you have been working with, I cannot comment on the figure you report. (as a side note, if you are working with Elekta data (and MEG field gradients), if I recall well you need to read in the gradiometer description specifying the ‘coilaccuracy’ option to be >=1 for the units to work well enough, otherwise the units may indeed be ill-defined).
Besides, the physical units of (MEG) leadfields should be something like T/nAm, or (T/m)/nAm etc. , so I am not sure why you mention the scale to be of ‘1e-10 T’.
This being said, correctly dealing with units is tricky, since different MEG/EEG vendors have different unit conventions (e.g. metric distances expressed in cm/m/mm, potentials expressed in muV or V etc). FieldTrip aims to work internally with SI units (i.e. m V T etc). To this end, it tries to apply the required scaling based on the specified units in the (metadata), or based on educated guesses from the dataformat. Also, FT tries hard to synchronize the units of the different data objects that are required for the computation (volume conductor, gradiometers)
However - to complicate things a bit more - , FieldTrip data structures (e.g. gradiometer descriptions with coil positions, gradient baseline lengths, and volume conductor models) are typically broadcasted to the user with units that may not be SI (e.g. MEG gradients in T/cm, volume conductor models in mm).
By the way, if you want to explore this further, I’d recommend you to compute the leadfields using ft_prepare_leadfield, since in this way you are closer to the actual computation (while still relying on FieldTrip’s bookkeeping functionality). Note that Marc’s e-mail on the discussion forum is already 8 years old, and I am pretty sure that quite some things have changed (for the better) in the mean time.
At this moment, I don’t see the need (yet) for any modification to the code, and I suggest that you explore a bit further, based on the above.
On 25 Apr 2022, at 15:30, Jasen Devasagayam via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
I ran into some confusion when looking at LCMV beamformed data, using the function, "ft_sourceanalysis". We are using a single shell forward model in these analyses. When looking at the output struct from this function, the lead fields were on the scale of 1e-10 T, which seems much too large for MEG fields. Looking into FieldTrip archives, I found a similar question by Marc Lalencette from 2014 (https://mailman.science.ru.nl/pipermail/fieldtrip/2014-September/008438.html) where it looks like the issue stems from the fact that fields are computed with respect to 'cm'.
I applied a conversion factor, by multiplying all data by 1e-4, to get from 'cm^2' to 'm^2'. I applied this conversion factor in the function "ft_compute_leadfield" in Line 260:
lf = lf*headmodel.forwpar.scale^2*1e-4;
I had originally tried to just adjust the scaling factor, but making that one small change severely altered the data in multiple places in our pipeline, which in turn yielded lead fields on the scale of 1e-10 once again. In this case, the scaling factor is 1.
I was wondering if this would be the correct place and method to implement this modification. If not, would you have any suggestions on how to get sensible lead field values?
Jasen Devasagayam, MASc
Research MEG Technologist
Neurosciences and Mental Health
The Hospital for Sick Children
686 Bay St., Toronto, ON M5G 0A4
P 416-813-7654 ext. 201535
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