[FieldTrip] AAL Surface plot - weird black spots

[Michał Komorowski]

Dear Fieldtrippers,

I found the solution and it is simple. Just make sure that you have in your
config follwing lines:

cfg.projmethod = 'project'
cfg.projvec = [0 5]

Have a nice plots !


Michał Komorowski, MSc
Nicolaus Copernicus University in Toruń
Faculty of Physics, Astronomy and Informatics
Department of Informatics

2017-07-31 14:15 GMT+02:00 Michał Komorowski <michak at is.umk.pl>:

> Dear Fieldtrippers,
>
> I am trying to reproduce brain surface pictures from this paper (Fig.5) :
> http://journals.plos.org/plosbiology/article?id=10.
> 1371/journal.pbio.1002498
>
> I wonder why I get weid black spots in surface plot (e.g. occipital area).
> What should I do to get those nice picures from link above?
> What I am doing wrong (code below)?
>
> Code for generating erroneous pictures (see attachment):
>
> mrifile             = [FieldtripPath 'template/anatomy/single_subj_
> T1.nii']
>
> mri = ft_read_mri(mrifile)
> mri.coordsys = 'mni'; % to prevent manual fixing of coordsys
>
> atlaspath       = [FieldtripPath 'template/atlas/aal/ROI_MNI_V4.nii'];
> atlas           = ft_read_atlas(atlaspath)
> atlas.anatomy   = mri.anatomy;
>
> cfg                     = [];
> cfg.method              = 'surface';
> cfg.projmethod          = 'project';
> cfg.camlight            = 'yes';
> %cfg.surffile = [FieldtripPath 'template/anatomy/surface_pial_left.mat'];
> % uncomment to project half brain
> cfg.locationcoordinates = 'voxel';
> cfg.cmap                = jet(116);
> cfg.cmap                = [[0,0,0]; cfg.cmap]
> cfg.funcolormap         = cfg.cmap;
> cfg.funparameter        = 'tissue';
> cfg.atlas               = atlaspath;
> ft_sourceplot(cfg, atlas)
>
>
> % check fit anatomy to atlas
> cfg                     = [];
> cfg.method              = 'ortho';
> cfg.locationcoordinates = 'voxel';
> cfg.cmap                = jet(116);
> cfg.cmap                = [[0,0,0]; cfg.cmap] % color map
> cfg.funcolormap         = cfg.cmap;
> cfg.funparameter        = 'tissue';
> ft_sourceplot(cfg, atlas)
>
> Best wishes.
>
> Michał Komorowski
>
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