Operating system: Windows 10 Slicer version: Slicer 4.8.1 Hi, I am writing a simulator which requires the registration of CT and MRI images. I am satisfied with Fiducial Registration; however, the steps required to perform this procedure may be intensive to the user (Registration -> Specialized ->…

Fiducial Registration module is a CLI module, which can be run from Python as described here: Documentation/Nightly/Developers/Python scripting - Slicer Wiki [image] Hikmat: I would like to automate this registration procedure (implement it programmatically) to simplify the U/I steps (I would s…

Did you found the method for automating the Fiducial Registryation with CLI?

Yes, I did. Apologies for not updating the status quo, it’s just that I’m still thinking about how I want to go about this.

Related question, How to use this module from cmd. It is not clear how to provide the landmarks as input ordered list arguments and it would be nice to add this to the module wiki. I tried: ~/sw/Slicer-4.8.1/Slicer --launch ~/sw/Slicer-4.8.1/lib/Slicer-4.8/cli-modules/FiducialRegistration --ret…

Here is a python script example: # create a transform node and add it to the scene transformNode = slicer.vtkMRMLLinearTransformNode() slicer.mrmlScene.AddNode(transformNode) parameters = {} parameters["saveTransform"] = transformNode.GetID() parameters["movingLandmarks"] = movingMarkupNode…

[image] brhoom: What is the correct format for providing the landmarks? You can run a CLI from the GUI and see in application log what command was used. If you enable developer mode in application settings then all input and output files are preserved after running a CLI module, so you can in…

see in application log Cool, this is really useful, in Ubuntu I found it in /tmp/Slicer-username/Slicer_version_date_time.log Here is an example of the arguments --returnparameterfile file.params --fixedLandmarks 1.854,-127.381,-260.861 --fixedLandmarks -3.282,-126.126,-261.026 --fixedL…

Automate Fiducial Registration

Development

Topic		Replies	Views
FIducial Registration Wizard through Python Interactor Support	8	1392	May 19, 2021
Set landmark registration parameters from command line python Development	1	261	March 20, 2020
Fiducial registration Wizard - custom transformation configuration Support markups-fiducials	18	1890	June 20, 2019
How to create a clone Fiducials then transform the original fiducials onto the clone fiducials Support markups-fiducials	13	1021	November 14, 2019
Automate model to CT registration Support registration	1	382	June 26, 2020

Automate Fiducial Registration

Related topics