[FieldTrip] Source Point Count & Atlas Point Count Discrepancy

[Konstantinos Tsilimparis]

Dear Sarah,

I would first recommend verifying that the coordinate systems and units of your atlas and template MRI are consistent. However, this does not appear to be the issue in your case.

The likely cause of the discrepancy is that out of the 6871 dipoles marked as “inside” the brain , there are regions such as the brain ventricles and the brainstem. These regions are not part of the 116 AAL ROIs, as depicted in Figure 2 of this paper<https://www.researchgate.net/publication/350967572_A_Deep_Learning_Approach_to_Predict_Autism_Spectrum_Disorder_Using_Multisite_Resting-State_fMRI> (https://www.researchgate.net/publication/350967572_A_Deep_Learning_Approach_to_Predict_Autism_Spectrum_Disorder_Using_Multisite_Resting-State_fMRI). Furthermore, your 7.5 mm source model is relatively coarse, and the boundary between "inside" and "outside" is not well-defined, leading to points that are “inside” the brain not assigned to any AAL ROI.

To visualize this better, you can plot the atlas-interpolated source model using the following code:

cfg = [];

cfg.funparameter = 'tissue';

cfg.funcolormap = 'jet';

ft_sourceplot(cfg, sourcemodel2);

Additionally, by specifying cfg.method = 'surface';, you can check the brain surface. You will observe that some boundary points are not assigned to any AAL ROI (e.g., note the dark blue spots on the occipital lobe):

cfg = [];

cfg.method = 'surface';

cfg.funparameter = 'tissue';

cfg.funcolormap = 'jet';

ft_sourceplot(cfg, sourcemodel2);



Best regards,

Konstantinos Tsilimparis



From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Sarah via fieldtrip
Sent: Wednesday, July 3, 2024 11:13 PM
To: fieldtrip at science.ru.nl
Cc: Sarah <s83728498 at gmail.com>
Subject: [FieldTrip] Source Point Count & Atlas Point Count Discrepancy


Hi all,



I have a question about mapping source points to atlas ROIs.



I have computed my source analysis using FT’s 3D grid of 7.5mm. I have also interpolated the FT shipped AAL atlas (ROI_MNI_V4.nii) onto this 7.5mm template grid.



I have now been mapping only some relevant source points to the atlas to determine which ROI they exist in. However, I noticed that many of my source points didn’t “exist” within the atlas. In fact, the # of my subject’s source points that exist inside/outside are reported as: 6871 dipoles inside, 6791 dipoles outside brain, whereas I notice the atlas interpolated source model only has 3475 points total.



I was wondering how to handle this apparent discrepancy (as I assume the atlas point count should at least be somewhat closer to the total of source points marked as inside the brain).



Thanks,

Sarah



P.S. I included some of my relevant code below to produce this, but it is simply the code of the FT tutorials.



Subject Sourcemodel Code:

cfg           = [];

cfg.method    ='basedonmni';

cfg.template  = template_grid;

cfg.nonlinear = 'yes';

cfg.mri       = mri;

cfg.unit      ='mm';

grid          = ft_prepare_sourcemodel(cfg);



Interpolate Atlas Code:

cfg = [];

cfg.interpmethod = 'nearest';

cfg.parameter = 'tissue';

sourcemodel2 = ft_sourceinterpolate(cfg, atlas, template_grid);

sourcemodel2 = ft_convert_units(sourcemodel2, 'mm');
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20240704/495c2d87/attachment.htm>