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Bug 804 - some MEG channels do not have correct coil positions and orientations

Reported 2011-07-07 17:23:00 +0200
Modified 2011-11-11 11:19:56 +0100
Product: FieldTrip
Component: yokogawa
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P1 normal
Assigned to: Kaoru Amano
Depends on:
See also:

Robert Oostenveld - 2011-07-07 17:23:02 +0200

the following channels in hdr.grad seem to have incorrect coil positions 'RM401' 'RM402' 'RM403' 'RM404' 'RM405' 'RM406' 'RM407' 'RM408' 'RM409' 'RM410' 'RM411' 'RM412'

Kaoru Amano - 2011-07-16 11:00:55 +0200

Which data file are you talking about? I think the loading function itself is fine and the position of some sensors is wrong even before we load the date into FT. So I don't think it's necessary to fix FT codes.

Tilmann Sander-Thommes - 2011-07-18 12:44:22 +0200

Created attachment 101 pciture of yokogawa software

Tilmann Sander-Thommes - 2011-07-18 12:45:04 +0200

The "RMx" refers to reference magnetometer sensors about 15 cm aways from the helmet, but within the Dewar. Yokogawa does not give location and orientation for them in the software (MEG160 -> Edit -> Channel Info: See attached figure). The RMs were included upon the wish of Vladimir / SPM to have all possible sensors. The RMs in other Yokogawa systems have position and orientation. If the absence of pos/ori causes trouble they should probably be removed at some stage. Till

Kaoru Amano - 2011-07-29 12:55:03 +0200

Today, I talked to a Yokogawa person, and he mentioned that they couldn't calibrate the location and orientation of reference sensors though they tried to do so. Robert, what do you think is the best way to deal with the Yokogawa reference sensors, whose position and orientation are not available.

Tilmann Sander-Thommes - 2011-10-17 17:28:00 +0200

Hi Robert, The question of the missing Yokogawa Reference Magnetometer positions is still open. I suggest to remove them from the grad-structure as they cannot be used in a forward calculation. To force a decision here I will remove them from the grad-structure if nobody objects. Yours, Till

Kaoru Amano - 2011-10-18 04:45:40 +0200

Just to make sure, FT doesn't give an error when we load the data of reference sensors, which is not defined in grad, right? I don't use reference sensors for now, but might use them for noise reduction in the future.

Tilmann Sander-Thommes - 2011-10-18 11:14:56 +0200

Hi Kaoru, If you to use the reference channels for noise reduction you load all channels in ft_preprocessing and then you can do the denoising. If you use SPM straight away you would not do denoising and then you are fine with gradiometer channels only. Is that correct and do you plan it that way ? Yours, Till

Kaoru Amano - 2011-10-18 12:24:56 +0200

If all the functions in FT don't complain about the data structure including the channels without the definition in data.grad.label, removing Yokogawa Reference Magnetometer positions is fine for me.

Tilmann Sander-Thommes - 2011-10-20 17:29:12 +0200

Dear Kaoru, I am still struggling with channel sequences from your system. I will attach a file, which I believe is originally from you. But it does not have any reference channels at all (MEG160 -> Edit -> Channel Info). Can you attach here a small file with your current (final ?) channel arrangement including reference channels, if there are any ? Many thanks, Till

Tilmann Sander-Thommes - 2011-10-20 17:30:10 +0200

Created attachment 168 yokogawa data file file wrt previous comment

Robert Oostenveld - 2011-10-21 15:40:57 +0200

using the attached test file, I have made the script test_bug804 which basically contains cd /home/common/matlab/fieldtrip/data/test/bug804 cfg = []; cfg.dataset = 'amano.ave'; data = ft_preprocessing(cfg); ft_plot_sens(data.grad); the script now runs through without a problem, hence I changed the status into "worksforme"

Robert Oostenveld - 2011-11-11 11:19:56 +0100

I closed all bugs that were recently resolved.