Motor tracteography with nTMS ROIs

Hey there!
I am trying to visualise the CST running from the nTMS positive points ( DICOM converted into .mif with mrconvert) optioned form the same patients and the brainstem as a ROI, but I am having problems doing this:

Should I do a whole brain tractogram and try to extract the desired tracks or directly generate only the tracks I am interested in?

How do I establish the brainstem as a ROI? Setting the real-world positions as vectors does not work. I get the notification that the "required input file “-x” (number) not found.
I have read that a binary mask can be done but I don’t know how.

Maybe you can help with that! I would be very thankful!
Thank you!

Hi @TPneuro,

Should I do a whole brain tractogram and try to extract the desired tracks or directly generate only the tracks I am interested in?

This is a topic that has been discussed many times on this forum, though admittedly it may be difficult to figure out the right search terms in order to discover such. I would summarize as follows:

  • If only wanting to reconstruct the spatial extent of a pathway of interest, direct generation of only the tracks of interest is more computationally efficient; but be wary of false negatives.

  • If wanting to perform quantitative connectivity analysis, a whole-brain tractogram is necessary.

There will be a better explanation of why this is the case when @jdtournier gives me feedback on my manuscript :pleading_face:

How do I establish the brainstem as a ROI? Setting the real-world positions as vectors does not work. I get the notification that the “required input file “-x” (number) not found”.
I have read that a binary mask can be done but I don’t know how.

It’s difficult to provide an interpretation of that notification without being provided with your full usage of the command. However as described in the tckgen help page:

... as a sphere using 4 comma-separared values (x,y,z,radius)

So for instance a ROI at location X=0mm, Y=10mm, Z=-50mm, with radius 20mm would be:

tckgen ... -include 0,10,-50,20 ... 

Binary mask images can be derived in a very broad number of ways. In your case I suspect you’re looking for manual definition of such rather than any clever image processing. So I would suggest opening mrview on your image data, go to “Tools” (top right) -> “ROI Tool”, click the “+” button to create a new ROI, click the “Edit” button in the ROI toolbar, and then click the left mouse button in the main window to start drawing. Once you see yellow squares appearing on top of your image, hopefully that’s enough to get you utilising the interface enough to progress with your actual experiment.

Cheers
Rob