Tractography interactive seeding in CLI module

Development
1

Hello Developers,

First of all Thank you for the support. I made some progress in my current task. I have implemented UKF tractography and add some modifications on it which I needed.

Now I want to implement interactive seeding tractography module as CLI. I am trying to implement it like this:

  def dti2fibers(self,markup,b):

if not hasattr(self, 'tractography_node'):
  self.tractography_node = slicer.vtkMRMLFiberBundleNode()
  slicer.mrmlScene.AddNode(self.tractography_node)

parameters = {
  'InputVolume': self.DTISelector.currentNode(),
  'OutputFibers': self.fiberBundleSelector.currentNode(),
  'InputFiducialList':self.markupSelector.currentNode() # THIS IS THE POINT OF ERROR
}

self.seeding_parameter_node = slicer.cli.run(
slicer.modules.tractographyinteractiveseeding, None,
parameters,wait_for_completion=False)

I am not sure about the input parameters? how can I give my markup node as an input to the module.
I saw the docuemntetion: https://www.slicer.org/wiki/Documentation/Nightly/Modules/TractographyInteractiveSeeding

But the inputs are not mentioned as clear as in ROI module : https://www.slicer.org/wiki/Documentation/4.10/Modules/TractographyLabelMapSeeding

Can you please let me know how can I give markup node as an input to my interactive seeding module.

Thank you so much

2

:smile:

To help people help you, could you include the specific error message? Also if you can point to a github repository of the full code it’s better than just including a snippet (so people can see where variables are defined, etc).

3

Hello Thank you fro your response. This snippet is general implementation from my source code. I am actually asking about the CLI parameters for tractographyinteractiveseeding module.

For ROI module it is clearly mentioned in documentation with the names:

Input DTI Volume** (InputVolume): DTI volume in which to seed (generate) tractography.
Input Label Map** (InputROI): Label map defining region for seeding tractography.
Output Fiber Bundle** (OutputFibers): Tractography result

But for Interative seeding module there is no such thing mentioned in the documentation.

I hope I am clear with my question. Sorry for the confusion.

4

What is your goal? Have you looked at the interactive UKF module?

5

I actually want to make a simple interactive tractography with simple mouse clicking which I have already implemented with ukf tractography.
Now I want to implement the same thing with interactive seeding module as ukf is computationally expensive.

I want to learn how to use interactive seeding module in CLI. I have tried to make a function but I dont know the CLI parameters it needs.

6

But does the Interactive UKF module already work for your needs?

Also, all CLIs should be able to print their help information when run on the command line with -h. This should help understand inputs.

7

It worked but it might be computationally expensive,

Also, I want to run tractography module on background. I could not figure out a way to run the whole UKF tracktography on background,

Typically on any CLI module we can this flag: set wait_for_completion=False

Thank you for your response.

8

Did you try the autorun options for the CLI?

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9

Thank you for your response, I have implemented UKF on my own application. I will try to activate it pragmatically. Thank you