Dear Don,
The differences you are referring to might have to do with the fact
that all fileio MEG readers represent gradiometers in head
coordinates. This is quite handy. For instance in SPM8 you can create
2D projections without the need to coregister sensors with the head
(see my recent discussion with Jerome about this). Also it makes it
possible to use the same coregistration for the whole session as long
as the localization coils are in the same place.
I might well be that there are some features in the code you have that
can complement the existing readers and that's what Jan-Mathijs in
particular can tell you because he is the main developer of BTi
support for fileio. Note, that you do not have to be a Fieldtrip
expert to contribute to this code. The fileio toolbox just collects
different format-specific readers under a common (and quite simple)
API that is described in one of the links below. It is our decision
in transition from SPM5 to SPM8 to only use fileio for conversion
(except for arbitrary data and Fieldtrip data, see the SPM8 manual).
So we would not be interested in readers that convert data to SPM8
format directly. On the contrary that'd be a headache for us as we
would like to have the freedom to change the internal format whenever
we feel like it while keeping the interface of MEEG object methods.
Best,
Vladimir
On Tue, Nov 11, 2008 at 10:12 PM, Rojas Don <[log in to unmask]> wrote:
> Vladimir,
>
> I'm happy to share whatever I come up with. I've imported several of my
> datasets, from a 248 channel 1st order gradiometer system, using the spm8
> convert routine to compare to my own function. I notice that there are a
> number of errors with respect to the channels and other aspects of the spm8
> converted files. For example, in the 4D headframe, +x is anterior and +y is
> left. So, in my own converter function, which I'm glad to forward if anyone
> is interested, the x and y from the 4D are swapped and the 4D +y becomes -y
> before the swap (all assuming that spm represents +y anterior and +x right,
> which is how I read the coordinates from the EEG templates and example
> files. I am using Eugene Kronberg's pdf4D object to perform the reading
> from the 4D raw files. I believe that his code has been incorporated into
> Fieldtrip, but I'll need to dig into the convert code in spm8 to see what's
> going on. I'm not a Fieldtrip user myself, so I cannot say for certain how
> it incorporates Eugene's code.
>
> Best,
>
> Don
>
>
> On 11/11/08 2:26 PM, "Vladimir Litvak" <[log in to unmask]> wrote:
>
>> Dear Don,
>>
>> SPM is perfectly capable of converting 4D-BTi format. Perhaps you
>> should just try the 'Convert' button. As I remember you have a lot of
>> experience with converting BTi data so perhaps you can contribute to
>> SPM8 (and also Fieldtrip) by contributing to the BTi readers included
>> in the fileio toolbox. Robert Oostenveld and Jan-Mathijs Schoffelen
>> (in CC) would be the key people to talk to about this. But perhaps you
>> should start with checking out the existing functionality.
>>
>> You can also find additional information at:
>>
>> http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:development:fileio
>> http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:freq
>> uently_asked_questions#how_are_electrodes_magnetometers_or_gradiometers_descri
>> bed
>>
>> Best,
>>
>> Vladimir
>>
>> Robert Oostenveld" <[log in to unmask]>
>>
>> On Tue, Nov 11, 2008 at 8:05 PM, Rojas Don <[log in to unmask]> wrote:
>>> Dear list,
>>>
>>> I am putting the finishing touches on a converter for the 4DNeuroimaging
>>> Magnes MEG system into the new SPM8 format and have a couple of questions:
>>>
>>> 1) How does the format represent the sensor geometry (i.e., magnetometer,
>>> gradiometer, planar gradiometer)?
>>>
>>> 2) What does the tra field in D.sensors.meg represent?
>>>
>>> I'll probably have a few more, but I thought I'd start with those.
>>>
>>> Best,
>>>
>>> Don Rojas
>>>
>>> --
>>> Donald C. Rojas, Ph.D.
>>> Associate Professor of Psychiatry and Neuroscience
>>> Director, Magnetoencephalography Laboratory
>>> University of Colorado Denver
>>> Department of Psychiatry, Mail Stop F-546
>>> Anschutz Medical Campus, Building 500 N2224G
>>> 13001 E 17th Place
>>> PO Box 6508
>>> Aurora CO 80045-0508
>>> 303-724-4994
>>> [log in to unmask]
>>>
>>> Please note: My email address has changed from [log in to unmask] to
>>> [log in to unmask] Please update your records.
>>>
>
> --
> Donald C. Rojas, Ph.D.
> Associate Professor of Psychiatry and Neuroscience
> Director, Magnetoencephalography Laboratory
> University of Colorado Denver
> Department of Psychiatry, Mail Stop F-546
> Anschutz Medical Campus, Building 500 N2224G
> 13001 E 17th Place
> PO Box 6508
> Aurora CO 80045-0508
> 303-724-4994
> [log in to unmask]
>
> Please note: My email address has changed from [log in to unmask] to
> [log in to unmask] Please update your records.
>
>
|