Hello Nasia,
see below.
> A) The number of samples I use in tractography is the default (5000). Does that mean 5000 samples PER VOXEL? Meaning for ROI1 in total 5000x123 and for ROI2 in total 5000x110?
Yes, that’s correct.
> B) For each of my subjects I get a waytotal file. One such files contains these numbers:
> 5991
> 3888
>
> My understanding is that beginning in ROI1 5991 streamlines reached ROI2, while beginning from ROI2 3888 streamlines reached ROI1. Is this correct?
> Is this the way the waytotal calculated: waytotal=(#voxels in ROI1 * #samples per voxel) - streamlines that did not reach ROI2 ?
Yes, that’s correct assuming that you did not specify any other waypoint or exclusion masks.
> C) When I open the fdt_paths.nii.gz image with fsleyes or fslview, are the min and max intensity values of each voxel in any way related to the # samples or streamlines that passed through that voxel? How should the intensities be interpreted?
Yes, the fdt_paths file contain the raw number of streamlines that go through each voxel.
Hope this helps, cheers,
Matteo
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