Incorrect coordinates?

[Jared Van Snellenberg]

Hi Robert,

I finally had time to edit the page you suggested.

-Jared


On 10/25/06, Robert Oostenveld <r.oostenveld at fcdonders.ru.nl> wrote:
>
> Hi Jared,
>
> Thanks for your detailled feedback. I think that it is a good idea to
> document these steps for other BESA users. I am rather busy, but
> maybe you could do it yourself? The FieldTrip website is a Wiki, and
> anyone can edit and contribute to it by pressing the "edit this page"
> button that you see on every page. Regarding this information: I
> would put it under a subheading (with some introductory comments,
> which probably can be copied-pasted from our previous mails) on the
> BESA-related page, i.e. on http://www2.ru.nl/fcdonders/fieldtrip/
> doku.php?id=fieldtrip:documentation:integrating_with_besa
>
> best regards,
> Robert
>
>
> On 23 Oct 2006, at 22:28, Jared Van Snellenberg wrote:
>
> > Hi Robert,
> >
> > I just wanted to let you know that your suggestion was correct (I
> > was working on a deadline for Friday, otherwise I would've
> > responded sooner), the problem was created by the fact that the out
> > of brain voxels were not masked out in the BESA data. The results
> > of the analysis after masking appropriately were drastically
> > different, and were all within-brain and make sense in light of the
> > experimental task.
> >
> > I used the following code to obtain the mask:
> >
> > inside=[];
> >
> >
> > for k=1:length(files)
> > src(k)=besa2fieldtrip([
> >
> > files(k).name]);
> > in=find(src(k).avg.pow);
> >
> > inside(end+1:end+length(in))=in;
> >
> >
> > end
> > inside=unique(inside);
> >
> > outside=1:49708;
> >
> > outside(inside)=[];
> >
> >
> > for k=1:length(files)
> > src(k).inside=inside;
> >
> > src(k).outside=outside;
> >
> >
> > endThis ensured that all the subjects had the same mask, and only
> > values that were 0 in all the subjects were masked out. I manually
> > checked all the subjects and there was at most a difference of 3 in
> > the number of nonzero voxels in any two subjects.
> >
> > You might want to document this somewhere for other users, as it's
> > not immediately apparent that specification of the .inside
> > and .outside fields in the source structure are critical for
> > further processing steps to behave correctly.
> >
> > Thanks for your help,
> >
> > -Jared
> >
> >
> >
> >
> > On 10/16/06, Robert Oostenveld <r.oostenveld at fcdonders.ru.nl>
> > wrote: Hi Jared,
> >
> > On 15 Oct 2006, at 0:12, Jared Van Snellenberg wrote:
> > > I've rerun the analysis with mri's that were reoriented to MNI, and
> > > the same problem has emerged.
> >
> > I would guess that the anatomical MRIs themselves do not influence
> > the coordinate system of the source reconstruction. That would
> > influence the interpolation though.
> >
> > If you do
> >   source = besa2fieldtrip(filename1)
> > and
> >   mri = read_fcdc_mri(filename)
> > then the source structure is defined using the source.pos field that
> > describes the position of each source. SInce in this case the
> > positions are on a regular 3D grid, there is additional structure in
> > the arrangement of source.pos, which is described using source.xgrid,
> > source.ygrid, source.zgrid.
> >
> > If you do
> >   tmp = reshape(source.avg.pow , source.dim)
> > you will get a 3D array with along the first dimension the voxels
> > along the x-axis, etc. The 1..Nth voxels along the xasix have the X
> > coordinates source.xgrid(1)..source.xgrid(N). Similar for the Y and Z
> > coordinates. That allows you to determine the coordinate of each
> > voxel.
> >
> > Since the anatomical MRI is typically of much higher resolution, you
> > can use sourceinterpolate which interpolates the source (or stat)
> > volumes onto the voxel locations that are in the anatomical MRI. I.e.
> > sourceinterpolate upsamples the functional data to the anatomical
> > MRI. Normally you would do sourceinterpolate AFTER calling
> > sourcestatistics, since the source positions in all subjects are all
> > based on the same standard realistic head moidel in BESA and hence
> > the source positions in all subjects are the same (please check
> > whether positions are all the same over subjects/conditions).
> >
> > If you work with MEG or with EEG individual headmodels, the source
> > positions in all subjects are all different, which requires
> > sourceanalysis->sourceinterpolate->volumenormalize as shown in the
> > schema for http://www2.ru.nl/fcdonders/fieldtrip/doku.php ?
> > id=fieldtrip:documentation:analysis_protocols#source_reconstruction_fo
> > r_
> > multiple_subjects
> >
> > > The typo you noted in your last email was indeed the reason for the
> > > empty src plot. Plotting src, interp, volume, and grandavg,
> > > everything looks ok. The 'pow' parameter values all appear within
> > > the brain. The tscore and p values in stat, however, are all messed
> > > up. I've attached .bmp's from using sourceplot on grandavg and stat
> > > to this email. The quality is poor (matlab's figure window doesn't
> > > ever save bmp's very well), but it should demonstrate the problem
> > > clearly. Note all the large values outside of the brain.
> >
> > In your case you should be able to do besa2fieldtrip ->
> > sourcestatistics, and then the source positions with the statistical
> > data on them should stll be the same as the positions with the
> > original functional data on them. After doing the statistics (or
> > after doing sourcegrandaverage), you can interpolate the functional/
> > statistical data onto the MRI. But since the statistical data and the
> > functional (beamed power) data are on the same coordinates, there
> > should not be a difference between them.
> >
> > > Any comments you have would be greatly appreciated. I've considered
> > > just masking out everything that's not in the brain, but I'm not
> > > confident that the within-brain values are accurate.
> >
> > Looking at the bitmaps, I cannot see teh anatomy, but I do see a
> > brain-shaped outline with some blobs in them. I cannot recognise the
> > problem from these figures, to me they seem ok. The only problem that
> > I can see is the one that you also mention, and that is for the
> > masking. In the original source data (i.e. output from
> > besa2fieldtrip) there is an source.inside and source.outside field.
> > Those should contain the indices of the voxels (linear indices, so
> > voxel [1 1 1] has index 1 and voxel [2 1 1] has index 2...) of the
> > sources that are inside the brain and outside the brain. Only the
> > inside voxels are considered for sourcestatistics and for
> > sourceinterpolation. However, the problem with BESA data is that it
> > does not describe the inside/outside voxels and therefoer by default
> > all voxels are marked as inside. Perhaps you can determine the inside/
> > outside voxels manually, e.g.
> >   source.inside  = find(source.avg.pow(:)>eps);
> >   source.outside = find(source.avg.pow(:)<eps);
> > After fixing the inside/outside, you can rerun sourcestatistics and
> > the rest. See the related FAQ http://www2.ru.nl/fcdonders/fieldtrip/
> > doku.php?
> > id=fieldtrip:documentation:frequently_asked_questions#why_is_there_a_r
> > im
> > _around_the_brain_for_which_the_source_reconstruction_is_not_computed
> >
> > To me it seems that the outside brain mess is caused by an
> > interpolation artifact, which can well be explained by the missing
> > inside/outside specification of besa. After fixing the inside/outside
> > vectors in the source structure, and passing it through
> > sourceinterpolate, you will get an interp.inside 3D boolean volume
> > with 0s and 1s for outside and inside voxels. You can element-wise
> > multiply the data with it, to mask the outside, or you can specify
> > cfg.mask='inside ' in sourceplot (which uses opacity).
> >
> > Hope this helps, if not, please put some data (source, mri, stat,
> > interp) in a zip file on ftp://ftp.fcdonders.nl/pub/incoming
> >
> > Robert
> >
> >
> >
> > --
> > Jared Van Snellenberg
> > Social Cognitive Affective Neuroscience Unit
> > http://scan.psych.columbia.edu
> > (212) 854-7858 p
> > (212) 854-3609 f
> > Department of Psychology, Columbia University
> > 406 Schermerhorn Hall
> > 1190 Amsterdam Avenue, Mail Code 5501
> > New York, NY 10027
>



--
Jared Van Snellenberg
Social Cognitive Affective Neuroscience Unit
http://scan.psych.columbia.edu
(212) 854-7858 p
(212) 854-3609 f
Department of Psychology, Columbia University
406 Schermerhorn Hall
1190 Amsterdam Avenue, Mail Code 5501
New York, NY 10027
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