Fiber tracking - ROI to ROI with passing Fibers

[Miguel Parra]

Hello!

We are trying to get tract information using ROIs. We would like to be able to capture tracts that begin and end in our ROIs, as well as capture information about tracts that pass through both regions.

However, with tracts that pass through both regions and do not terminate in either, we would like to trim those tracts down to only include the parts that pass through both ROIs, as if they terminate in said ROIs.

Here is a crude diagram attempting to explain what I mean. Tracts 1 and 2 we are able to measure, but tract 3 (with trimming) is eluding us.

The best way we have right now is to create terminative regions around the ROIs that allow Tract 1 to be included, but exclude tracts that exit ROI 1 and 2 and do not terminate in the paired ROI region.

Thank you!

Miguel

[Frank Yeh]

You may use 'roi'+'not end' to get only the passing fiber. 

Then use two end regions to get the ending fibers.

Frank

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[Miguel Parra]

This doesn't quite do it, we're looking to trim the excess off the passing fibers. Is there a programmatic way to do that without defining terminative regions manually?

[Miguel Parra]

That almost gets it, but we are still having issues with #3. Namely, the fiber isn't being "cut".

We know that through certain ROIs there are passing fibers, but we would like to trim them such that they appear to terminate in our defined ROIs. We can do this manually by placing terminating planes outside of the ROIs, but this is tedious and we'd like to know if there is a programmatic way to approach this.

On Tuesday, July 1, 2025 at 1:56:15 PM UTC-7 Frank Yeh wrote:

[Frank Yeh]

I would try converting tract2 to ROI, dilate it a bit, negate it, and set it as terminative region.
Would you like to achieve this using CLI or command history?

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