[FieldTrip] unit problem when following example script: Create MNI-aligned grids in individual head-space BUG?

[Ayelet Landau]

Hi all,

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.

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.

greetings from Frankfurt,

Ayelet and Barbara




On Fri, Apr 12, 2013 at 8:06 AM, Diego Lozano Soldevilla <
d.lozanosoldevilla at fcdonders.ru.nl> wrote:

> Hi Ingrid,
>
> I had similar problem with MEG and  changing the units with
> ft_convert_units solved the issue:
>
> vol = ft_convert_units(vol,'cm')
>
> If not, please file a bug with a piece of data and I'll have a look,
>
> best,
>
> Diego
>
>
>
>
> On 11 April 2013 20:30, Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu>wrote:
>
>> Hi all,
>>
>> 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.
>>
>> 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.
>> template_grid =
>>       xgrid: [1x41 double]
>>       ygrid: [1x41 double]
>>       zgrid: [1x41 double]
>>         dim: [41 41 41]
>>         pos: [68921x3 double]
>>        unit: 'mm'
>>      inside: [1x68910 double]
>>     outside: [758 759 760 761 799 800 801 802 843 884 925]
>>         cfg: [1x1 struct]
>>
>> 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?).
>>
>> So, it looks like a bug to me, or am I doing something wrong? I'm using
>> the newest FT version.
>>
>> Thanks,
>> Ingrid
>>
>> %%% CODE FROM WIKI %%%
>> template          = ft_read_mri([cur_path_FT 'external', filesep, 'spm8',
>> filesep,'templates', filesep,'T1.nii']);
>> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the
>> coordinate system
>>
>> % segment the template brain and construct a volume conduction model
>> (i.e. head model): this is needed
>> % for the inside/outside detection of voxels.
>> cfg          = [];
>> template_seg = ft_volumesegment(cfg, template);
>>
>> cfg          = [];
>> cfg.method   = 'singleshell';
>> template_vol = ft_prepare_headmodel(cfg, template_seg);
>>
>> % construct the dipole grid in the template brain coordinates
>> % the source units are in cm
>> % the negative inwardshift means an outward shift of the brain surface
>> for inside/outside detection
>> cfg = [];
>> cfg.grid.xgrid  = -20:1:20;
>> cfg.grid.ygrid  = -20:1:20;
>> cfg.grid.zgrid  = -20:1:20;
>> cfg.grid.unit   = 'cm';
>> cfg.grid.tight  = 'yes';
>> cfg.inwardshift = -1.5;
>> cfg.vol        = template_vol;
>> template_grid  = ft_prepare_sourcemodel(cfg);
>>
>> % make a figure with the template head model and dipole grid
>> figure
>> hold on
>> ft_plot_vol(template_vol);
>> ft_plot_mesh(template_grid);
>>
>> --
>> Ingrid Nieuwenhuis PhD
>> Postdoctoral Fellow
>> Sleep and Neuroimaging Laboratory
>> Department of Psychology
>> University of California, Berkeley
>> California 94720-1650
>> Tolman Hall, room 5305
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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-- 
Ayelet N. Landau

Postdoctoral Scientist,
Ernst Strüngmann Institute (ESI) for Neuroscience
in Cooperation with Max Planck Society
Deutschordenstr. 46, D-60528 Frankfurt

Mobile:      +49 (0)16 22733 110
Fax:      +49 (0)69 96769 555
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