<div dir="ltr">Hi Ingrid,<div><br></div><div style>I had similar problem with MEG and changing the units with ft_convert_units solved the issue:</div><div style><br></div><div style>vol = ft_convert_units(vol,'cm')<br>
</div><div style><br></div><div style>If not, please file a bug with a piece of data and I'll have a look,</div><div style><br></div><div style>best,</div><div style><br></div><div style>Diego</div><div style><br></div>
<div style><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 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 class="HOEnZb"><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>_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></div><br></div>