[FieldTrip] How do I use an atlas to find regions on an individual MRI?

[Andreja Kostić]

Hello dear Fieldtrippers!

This is my first post on the mailing list, so I apologize if this looks a
bit confused.



So I'm trying to use the WFU PickAtlas for Brodmann areas in what I think
are MNI coordinates to find specific regions inside of a brain (I'm coming
from electrical engineering background, so I can't do that "by hand") in an
individual whole-head MRI and I'm having issues getting sane results.

I suspect that my workflow is the problem, so I would be very grateful if
someone could provide some advice as to what I should be actually doing.

My original idea was to take MRI in CTF coordinates, convert it to MNI
coordinates and then just use atlas to make masks. From what I could
gather, it's not that simple.

So here are examples of what I'm doing right now:

ft_defaults;

%Let's read atlas

atlas =
ft_read_atlas('C:\REALY_LONG_PATH_TO_PICKATLAS\wfu_pickatlas\MNI_atlas_templates\TD_brodmann.nii');


%Using Subject01from FT tutorials right now, for simplicity's sake.
mri = ft_read_mri('Subject01\Subject01.mri');


%Reslice, apply transformations
cfg=[];
cfg.dim=[256 256 256];
mri_resliced=ft_volumereslice(cfg, mri);

cfg=[];
mri_norm1=ft_volumenormalise(cfg,mri_resliced);

%Unfortunately, this cuts off everything below the nose!

%Still let's take a look at the visualization with atlas

cfg=[];
cfg.inputcoord='mni';
cfg.atlas=atlas;
cfg.roi='brodmann area 4';

mask4 = ft_volumelookup(cfg, mri_norm1);
mri_norm1.mask4=mask4;

cfg=[];
cfg.atlas=atlas;
cfg.funparameter = 'mask4';
ft_sourceplot(cfg,mri_norm1)



%The result doesn't look so good, big part of the area seems to fit inside
of the gaps between brain tissue!

So this doesn't seem to have worked out. My next attempt was to directly
use ft_convert_coordsys. This fixed the cutting issue, but it didn't solve
the problem of results looking strange.

So my other idea was to try with

template=ft_read_mri('C:\PathToFT\external\spm8\templates\T1.nii');

cfg=[];
cfg.method='spm';
cfg.coordsys='spm';
mri_realigned=ft_volumerealign(cfg,mri_resliced,template);

But this produces very obviously wrong results, like coronal slices on
sagittal plane.

I'm also not sure if I should be trying to somehow transform an atlas to
fit the individual MRI that I'm using?

All the best,
Andreja Kostić
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