Create a tool that can convert tracked ultrasound sequences to CT volumes

[cpinter]

Create a tool that can convert tracked ultrasound sequences to CT volumes, for prostate HDR brachytherapy planning.

Sample script is available here: https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/sandbox/UsToCtConverterSample

The final solution should be something like this:

• A standalone executable, which uses Plus and DCMTK
• Plus is used to read the input ultrasound sequence metafile (mha) acquired using the Plus toolkit
• DCMTK is used to construct a sequence of CT slices that contain all the mandatory fields (the CT data set in the UsToCtConverterSample/originalCT directory contains some optional, private fields as well, so not all of them have to be included, only those required by the DICOM standard Part 3)
• Some fields are updated in the sample script (pixel data, image size, etc.), but some more fields would need to be updated in the final solution (at least new instance UID should be generated for each slice)

Optional:

• Would be nice to get the pixel spacing from the Plus configuration file (from the ImageToProbeTransform matrix)
• Would be useful to be able to burn in the centerline of reconstructed needle trajectories into the US image pixels to improve the catheter visibility
• Might be useful to support arbitrary image orientation (for freehand tracked US acquisition; by reconstructing an US volume)

Migrated from https://app.assembla.com/spaces/slicerrt/tickets/193-create-a-tool-that-can-convert-tracked-ultrasound-sequences-to-ct-volumes/details

[cpinter]

2012-12-04 22:17 Gabor Fichtinger We also need to get the US pixel size ; TRUS stepping is hard coded at 5mm.

Soon enough, we will have to calibrate the stepper and provide coordinate transformation from 3D TRUS space to Template Space. Not forgetting that the face of the template is not encoded – the bastards; we will have to put the calibrated grid onto the Ultrasonix display to guide the insertion.

2013-06-26 11:18 Csaba Pinter Assigned to set to Adam Rankin

2013-06-26 11:20 Adam Rankin Ah cool, didn't know there was a real ticket.

2013-06-26 11:27 Csaba Pinter No worries, I just bumped into it myself.

2013-09-06 14:57 Csaba Pinter Priority changed from Normal (3) to High (2)

2013-09-06 16:09 Gabor Fichtinger Is this a proper CT simulator or the fake generator for Chandra?

2013-09-06 16:16 Csaba Pinter It's the one Adam has been working on. Should be the fake one for Chandra.

2013-09-10 12:44 Adam Rankin Link to work in progress:

https://www.assembla.com/spaces/perklabsandbox/tickets/8#/activity/ticket:

2013-09-30 13:41 Adam Rankin Status changed from New to Test Tool is created and produces DICOM volumes. Testing is needed in Oncentra system.

2014-01-22 13:57 Csaba Pinter Has testing taken place?

2014-01-22 14:21 Adam Rankin No, this was going to be a project with Dr. Joshi. Probably someone else will have to coordinate with him to validate it. A student perhaps?

2014-01-22 17:05 Andras Lasso We had a meeting about this and related projects. We have to make it work soon. I'll check it when I'm back from vacation.

2015-01-16 00:10 Csaba Pinter Priority changed from High (2) to Low (4)

2015-06-15 15:42 Adam Rankin Assigned to changed from Adam Rankin to -none-