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Thanks both,<br>
<br>
I do agree it's a bug then, because the units are known to the
functions and they should not behave like this. The units should be
converted automatically, or an error should appear telling the user
to convert units to match. Anyway, a bugs already filed and a work
around is possible, so all good. By the way, I also found a way
around my self that might be useful for others to know. There are
templates in FieldTrip now (great all this pre-made stuff). So I
just did below, and voila :)<br>
<br>
Thanks, <br>
Ingrid<br>
<br>
%%% my work around %%%<br>
load('standard_sourcemodel3d7point5mm')<br>
<br>
% read the single subject anatomical MRI<br>
mri = ft_read_mri(['D:\FT_DATA\Subject01', filesep,
'Subject01.mri']);<br>
<br>
% create the subject specific grid, using the template grid that has
just been loaded<br>
cfg = [];<br>
cfg.grid.warpmni = 'yes';<br>
cfg.grid.template = sourcemodel;<br>
cfg.grid.nonlinear = 'yes'; % use non-linear normalization<br>
cfg.mri = mri;<br>
cfg.sourceunits = 'mm';<br>
grid = ft_prepare_sourcemodel(cfg);<br>
<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/12/2013 1:14 AM, Erik te Woerd
wrote:<br>
</div>
<blockquote
cite="mid:CAEGmzkiSJnKXVOvaHg7CzWGjMZoCv2Cu+DvBG+Exyx+=F4aPzg@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>
<div>
<div>Hi Ingrid,<br>
<br>
</div>
I also encountered this problem when following the
tutorial, but was able to solve it in the way Diego
suggests it below. While following the tutorial, all
variables should be returned with corresponding units, but
in ft_prepare_headmodel this doesn't work.<br>
</div>
I reported it already to bugzilla and it's being looked
after...<br>
<br>
</div>
Best,<br>
<br>
</div>
Erik<br>
<div>
<div>
<div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/4/12 Diego Lozano
Soldevilla <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:d.lozanosoldevilla@fcdonders.ru.nl"
target="_blank">d.lozanosoldevilla@fcdonders.ru.nl</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div dir="ltr">Hi Ingrid,
<div><br>
</div>
<div>I had similar problem with MEG and
changing the units with ft_convert_units
solved the issue:</div>
<div><br>
</div>
<div>vol = ft_convert_units(vol,'cm')<br>
</div>
<div><br>
</div>
<div>If not, please file a bug with a piece of
data and I'll have a look,</div>
<div><br>
</div>
<div>best,</div>
<div><br>
</div>
<div>Diego</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 11 April 2013
20:30, Ingrid Nieuwenhuis <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:inieuwenhuis@berkeley.edu"
target="_blank">inieuwenhuis@berkeley.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">Hi all,<br>
<br>
When I follow the code according to the
example matlab script "Create MNI-aligned
grids in individual head-space" something
goes all wrong with the units.<br>
<br>
I've followed the code (pasted below, from
the wiki), but when I make the figure with
the template head model and dipole grid,
it's wrong (see attached ..._problem.png).
The dipole grid is tiny in the bottom of
the head model. The black area is the
dipole grid, not good.<br>
template_grid =<br>
xgrid: [1x41 double]<br>
ygrid: [1x41 double]<br>
zgrid: [1x41 double]<br>
dim: [41 41 41]<br>
pos: [68921x3 double]<br>
unit: 'mm'<br>
inside: [1x68910 double]<br>
outside: [758 759 760 761 799 800 801
802 843 884 925]<br>
cfg: [1x1 struct]<br>
<br>
It's a problem with the units, because the
template grid has 'mm' in the unit field,
but when I look in the xgrid, ygrid, zgrid
and pos fields the numbers are clearly cm
not mm. However, when I multiply my
xyzgrid and pos field by 10, the grid is
not tight (see attached
..._multiplied10.png). It looks like the
unit problem messed up the determination
of what's inside and outside. As you can
see in the template_grid, there are only a
few grid point outside, which is clearly
not correct (maybe inside/outside was
determined on wrong units?).<br>
<br>
So, it looks like a bug to me, or am I
doing something wrong? I'm using the
newest FT version.<br>
<br>
Thanks,<br>
Ingrid<br>
<br>
%%% CODE FROM WIKI %%%<br>
template =
ft_read_mri([cur_path_FT 'external',
filesep, 'spm8', filesep,'templates',
filesep,'T1.nii']);<br>
template.coordsys = 'spm'; % so that
FieldTrip knows how to interpret the
coordinate system<br>
<br>
% segment the template brain and construct
a volume conduction model (i.e. head
model): this is needed<br>
% for the inside/outside detection of
voxels.<br>
cfg = [];<br>
template_seg = ft_volumesegment(cfg,
template);<br>
<br>
cfg = [];<br>
cfg.method = 'singleshell';<br>
template_vol = ft_prepare_headmodel(cfg,
template_seg);<br>
<br>
% construct the dipole grid in the
template brain coordinates<br>
% the source units are in cm<br>
% the negative inwardshift means an
outward shift of the brain surface for
inside/outside detection<br>
cfg = [];<br>
cfg.grid.xgrid = -20:1:20;<br>
cfg.grid.ygrid = -20:1:20;<br>
cfg.grid.zgrid = -20:1:20;<br>
cfg.grid.unit = 'cm';<br>
cfg.grid.tight = 'yes';<br>
cfg.inwardshift = -1.5;<br>
cfg.vol = template_vol;<br>
template_grid =
ft_prepare_sourcemodel(cfg);<br>
<br>
% make a figure with the template head
model and dipole grid<br>
figure<br>
hold on<br>
ft_plot_vol(template_vol);<br>
ft_plot_mesh(template_grid);<span><font
color="#888888"><br>
<br>
-- <br>
Ingrid Nieuwenhuis PhD<br>
Postdoctoral Fellow<br>
Sleep and Neuroimaging Laboratory<br>
Department of Psychology<br>
University of California, Berkeley<br>
California 94720-1650<br>
Tolman Hall, room 5305<br>
<br>
</font></span><br>
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<pre class="moz-signature" cols="72">--
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 </pre>
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