SPM2 and SPM5

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Fri Jan 23 17:57:47 CET 2009

Hi Wei,

On 21 Jan 2009, at 23:01, Wei Wang wrote:
> Hi FieldTrip friends,
> We're starting to use FieldTrip for our MEG data analysis.  The main
> problem I
> have is that the FieldTrip toolbox does not segment my MRI data
> properly,
> e.g. it will miss a lot of gray matters.  What would be the general
> suggestions
> for this type of problem?  Is it possible for me to fine tune the
> segmentation
> parameters.

At the FCDC we are not really experts in segmentation. The
volumesegment function contains defaults for SPM2 that work for our
anatomical MRIs, i.e. for the particular sequence used on our MRI
scanner whenever we send someone down to get a "MEG"-MRI. In SPM2/5/8
you of course have many more options for segmenting. The read_fcdc_mri
function will read in anatomical MRIs' but also segmented MRIs.

> Also, it seemed to me that FieldTrip uses SPM2 for the
> segmentation.  I'm
> wondering if FieldTrip is going to switch to SPM5 or not, assuming
> that SPM5
> is more recent than SPM2.

There were some inconsistencies in the interface to the functions
comparing SPM2 and SPM5, which is why we never swiched (and of course
also because SPM2 already does the segmentation trick for us). We
won't put effort into SPM5, but it is likely that the dependency on
SPM2 functions will be replaced by the corresponding SPM8 functions.
But it should also be easy to do the segmentation in SPM8 (e.g. with
DARTEL) and read in the result for head-model generation and further
processing in fieldtrip. MRI data formats are relatively simple to
support, only the coordinate system alignment can be tricky.

best regards,

The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

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