[FieldTrip] Mismatch between channel label and position in hdr.grad (Neuromag 306 system)

Hanneke van Dijk Hanneke.vanDijk at med.uni-duesseldorf.de
Mon Jun 25 11:01:22 CEST 2012


Dear Jarang,

Coincidentily I have been working on the same problem a few weeks ago.

First of all you should take care that you repair a horizontal gradiometer
with neighbouring horizontal gradiometers and vertical ones with vertical
ones. This is not built into fieldtrip yet.

I have have made a partial fix, which works with the 'layout' option but
not with the 'grad' method. I have attached the function I addapted from
Fieldtrip, and the layout files that seperatly name the different
gradiometers (made by Elisabeth May ;-) )

I hope it somehow helps you!

Best regards,

Hanneke van Dijk

________________________________________________________________


Hanneke van Dijk, PhD

http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html

Institute for Clinical Neuroscience,

Heinrich Heine Universität Düsseldorf, Germany

Hanneke.vanDijk at med.uni-duesseldorf.de

Tel. +49 (0) 211 81 13074

__________________________________________


On Mon, Jun 25, 2012 at 4:57 AM, Jarang Hahm <jarang.hahm at gmail.com> wrote:

> Dear FieldTrip user.
>
>
>
> Hi, I'm processing MEG data of Neuromag 306 system after removing some bad
> channels using fieldtrip-20120620 toolbox.
>
>
>
> To repair the bad channels with its neighbours, I firstly found the
> neighbor of all channel based on distance using 'ft_prepare_neighbours'.
>
> However, the outcome of neighbour was far more than default distance, 4cm,
> from a target channel.
>
> So, I checked thoroughly the code 'ft_prepare_neighbours', finding it used
> information of channel label and position from data’s hdr.grad to find
> neighbour of the target.
>
>
>
> The problem is channel label and position in hdr.grad are arranged
> differently.
>
> As far as I found, both information come from different source: the
> channel label was from code 'fiff_read_meas_info', while the channel
> position was from ‘channelposition’ in 'ft_datatype_sens'.
>
> And  the channel label is sorted into the sensor location, e. g. MEG 0113,
> MEG 0112, MEG 0111, MEG 0122, etc, however, the channel position is
> arranged along the sensor type (magnetometer and gradiometer) according to
> its ending number (1, 2, or 3), e.g. MEG 0111, MEG 0121, MEG 0131, ....,
> MEG 0112, MEG 0122, MEG 0132, ...MEG 0113, MEG 0123, MEG 0133, etc.
>
> Thus, the label and position of channel in hdr.grad were mismatched so
> that we got somewhat weired neighbour after using 'ft_prepare_neighbours'.
>
>
> It should be matched correctly to find the proper neighbour and ensure the
> result of repair as well.
>
> In fact, the code 'channelposition' in 'ft_datatype_sens' yield the
> channel label as well as the channel position. It might help to solve this
> problem.
>
>
>
> Is there any other way to solve this problem?
>
>
>
>
> Best,
>
>
> Jarang Hahm
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120625/ea2e149f/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: neuromag_prepare_neighbours.m
Type: application/octet-stream
Size: 1823 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120625/ea2e149f/attachment-0004.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NM306hor.lay
Type: application/octet-stream
Size: 5238 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120625/ea2e149f/attachment-0005.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NM306ver.lay
Type: application/octet-stream
Size: 5235 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120625/ea2e149f/attachment-0006.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: batch_channel_repair.m
Type: application/octet-stream
Size: 410 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120625/ea2e149f/attachment-0007.obj>


More information about the fieldtrip mailing list