Export the position of the nodes of a connectome

Hello Mrtrixers!

I’m working with the HCP tutorial and I have a couple of questions:

  1. Regarding Mrtrix command/scripts: I want to know if there is any automated way to retrieve the positions of the nodes of my connectome… I mean, with the mrview window I’m able to load the node parcellated image, its connectome and when selecting one particular node display the voxel information (including the position). But what I need is to get this information (the position) for all the connectome nodes.

  2. Newbie question regarding connectome. Once I had loaded the connectome nodes I’m capable of scroll over different slices of the image, but this not affect the displayed nodes. Is this the intended behaviour of the connectome display? Because I would expect them to change at different slice.

Thank you!


Hi Stella,

  1. Not currently; the mrview connectome tool calculates the node centres-of-mass as part of its initialization process when you import the parcellation image. It would however be a relatively trivial command to implement; e.g. labelstats could calculate the volume and centre-of-mass of each parcel within an integer label image. I could add this to the list of requests if you’d like.

  2. Yes, this is deliberate. I think that when people first load up the connectome tool, they expect to ‘see a connectome’; if only a slice were displayed, then the first loaded slice may be completely void of any connectome information; or it may just include some cut-through cross-sections of some grey spherical nodes, which would probably be counter-intuitive to most. So the connectome tool defaults to a 3D display, giving users an initial sense of feedback that ‘there’s a connectome there’ before they start experimenting further; but such a projection doesn’t change as you scroll through slices, and distant nodes are not ‘hidden’ by the displayed image slice as this would be more likely to cause confusion than to be of any use.
    You can alter the 2D/3D behavior in the ‘Miscellaneous options’ section of the connectome tool, by turning on ‘crop to slab’. But you probably want to have some connectome information loaded (e.g. connection densities from a connectome matrix, node colors from a lookup table file, node mehes) before you activate that option; otherwise you might get lost!