<div dir="ltr">Hi all,<div><br></div><div style>Barbara Händel and I have spent some time checking how deep this unit problem goes. I don't know if the bug control made it to this issue as of yet, but it occurs to us that this can be very easily controlled if one were to add a cfg.unit to ft_plot_mesh and ft_plot_vol.</div>
<div style><br></div><div style>evidently, the defaults for grid and the defaults for volume seem to be different (cm for the first mm for the latter and others). When you run the two plotting commands there is no way to propagate a "common scaling" since those are separate commands. Adding the units and having a single (common) unit for the output which is plotted would deal with this problem.</div>
<div style><br></div><div style>greetings from Frankfurt,</div><div style><br></div><div style>Ayelet and Barbara</div><div style><br></div><div style><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Apr 12, 2013 at 8:06 AM, Diego Lozano Soldevilla <span dir="ltr"><<a href="mailto:d.lozanosoldevilla@fcdonders.ru.nl" target="_blank">d.lozanosoldevilla@fcdonders.ru.nl</a>></span> wrote:<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"><div><div class="h5">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>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">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>
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<br>_______________________________________________<br>
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<br>Postdoctoral Scientist, <div>Ernst Strüngmann Institute (ESI) for Neuroscience<br>in Cooperation with Max Planck Society<br>Deutschordenstr. 46, D-60528 Frankfurt<br><br>Mobile: +49 (0)16 22733 110<br>Fax: +49 (0)69 96769 555</div>
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