Lost gray matter during segmentation

[Robert Oostenveld]

Hi Wei Wang,

I don't know about the underlying SPM2 methods to help you further. I
suggest that you ask on the SPM mailing list.

Note that the SPM2 toolbox on which these fieldtrip functions wqere
built is already old (SPM version 2 is from 2002, version 5 is from
2005 and later this year SPM8 will be released). These particular
functions in spm5 turned out to be not backward compatible. Since
sofar there seemed no reason to update the fieldtrip functions to use
spm5 (or spm8) instead of spm2, we have never upgraded to a later spm
version. It might be that your problem would be solved by later spm
versions. If that is the case, I would like to hear that, since that
would provide a good motivation for upgrading the fieldtrip code to
use the later spm versions instead of the old spm2.

best regards,
Robert


On 18 Sep 2008, at 5:48, Wei Wang wrote:

> Hi everyone,
>
> I'm trying to work with my own MRI data, and after I did the
> segmentation
> with volumesegment.m , when I examine the gray matter with
> sourceplot, it
> seems that fraction of the gray matter was not marked as gray
> matter.  They
> were left out for some reason.  For example, part of the visual
> cortex are not
> included in my gray matter.  Since the segmentation is done using
> SPM2, I
> read the SPM manual a little bit, and, in the manual, it says,
> "5.2.5 Clean up any partitions
> This uses a crude routine for extracting the brain from
> segmentedimages. It
> begins by taking the white matter, and eroding it acouple of times
> to get rid of
> any odd voxels. The algorithm continues on to do conditional
> dilations for
> several iterations,where the condition is based upon gray or white
> matter
> being present. This identified region is then used to clean up the
> grey and
> white matter partitions, and has a slight in uences on the CSF
> partition.
> If you find pieces of brain being chopped out in your data, then you
> may wish
> to disable or tone down the cleanup procedure."
>
> So, I went into the volumesegment.m code, and set:
> defaults.segment.write.cleanup   = 0;
>
> When I run volumesegment again, it seems to improve the results a
> little bit,
> but still, I'm loosing some gray matters.
>
> I'm wondering if you have any suggestions?  Thank you very much for
> the help!
>
> Wei Wang
> Department of Physical Medicine and Rehabilitation
> University of Pittsburgh
>
> ----------------------------------
> 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.
>

----------------------------------
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.