SPM integration

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Wed Nov 1 14:20:52 CET 2006

Hi Vladimir,

On 31 Oct 2006, at 15:06, Vladimir Litvak wrote:
> I'm starting to work on a project where I will analyze data
> preprocessed in FT with SPM5 (www.fil.ion.ucl.ac.uk/spm/). For this
> purpose I'd like to develop FT/SPM integration routines.
It would be really nice if you could work on that.

> I'll probably start with my immediate needs but I think I'm
> motivated enough at the moment to eventually turn it into something
> of general usefulness. If anyone has already worked in this
> direction and has some code or would like to collaborate please let
> me know.
I am not aware of anything substantial in this direction, except that
James Kilner and I have been exchanging emails about CTF dataformats
(it could be that he is using snippets of our code). Furthermore, I
know that Stefan Kiebel has integrated the EEG forward modelling code
from FieldTrip into SPM. I have CCd this mail to them.
> I'm affiliated to the methods group at FIL so I can get help from
> SPM developers if necessary. Right now I'd like to be able to use
> FT to read any FT supported format to SPM.
I have split off the import routines (the "fileio" part) that we use
in FieldTrip into a seperate package, already with the idea that
other projects (SPM, EEGLAB) can reuse and contribute to the reading
functions. So you can use the reading functions seperately from
FieldTrip. That means that you will not be using the cfg-structure
interface to the high-level FT functions, but that you will use the
lower level read_header/read_data/read_event functions.

See http://www2.ru.nl/fcdonders/fieldtrip/doku.php?

The download for the fileio functions is available from ftp://
ftp.fcdonders.nl/pub/fieldtrip/modules. I am considering moving the
FT version control system (esp. for the fileio and forwinv module) to
an external server (e.g. sourceforge) so that other people can
contribute. Sofar I did not find that neccessary, and all external
contributions go through email.
> Additional question: how does one create low-level routines for a
> new (rare) data format to be used by FT preprocessing? Is there a
> template or some interface they should adhere to?
I suggest that you look into read_header/read_data/read_event (in
fieldtrip/private), and that you pick one of the already supported
formats that you are familiar with as template. There is also some
(sparse) documentation on
Furthermore, I could dig up some old emails with additional
explanation (you are not the first to contribute data format specific
code), but I think that the info sofar should already get you
started. I will try to update the documentation on the FT wiki as well.

best regards,

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