Estimating tracts for a specific region

Hi All,

I am just wondering, if it is possible to tell if streamlines/tractography are from a specif ROI.

I would like to know, if it is possible to tell if a certain group of tracts belong to a certain region.

How can one determine if they are afferent or efferent connection between two specific subcortical regions.

For instance, can one identify tracts only specific between Globus pallidus external and internal ?


I think much of what you’re trying to do here can probably be done using tckedit: if any streamlines are selected when specifying an inclusion ROI, then these streamlines at least intersect with that ROI. You can also use the -ends_only option if you’re interested about whether the streamlines end in those regions.

That’s not something diffusion MRI can tell you. Diffusion is an inherently symmetric process, there’s no way to tell afferent from efferent…

If it be possible to generate a .nii file include the voxels of the inclusion ROI which the tracts passing through?

If I understand what you mean correctly, this should do it:

tckmap your_tracks.tck -template your_inclusion_ROI.mif - | mrcalc - your_inclusion_ROI.mif -mult final_map.mif

Essentially: use tckmap to create an image of streamline counts for your tracks in ROI space, then multiply that by your ROI image itself. Is this what you were after?

1 Like

You answer perfectly solved my question!

There is another question, what is the intensity value of the .mif generated from tckmap?(eg. the scale is from 0-3)

Good to hear. By default, it’s simply the number of streamlines going through each voxel.

I see, thanks again!