Changing window/level and index slice for a volume loaded from the command line

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1

Hi,

I am trying to write a piece of code that will open the Slicer GUI from the command-line, and load a particular volume, with a chosen window/level, and some fiducials pre-loaded into the scene. The code below partially works, in that it loads the volume and fiducials, but I can’t get the window/level change to work.

/Applications/Slicer\ 2.app/Contents/MacOS/Slicer \
--python-code "volumeNode = slicer.util.loadVolume('200056.nrrd', returnNode=True); displayNode = volumeNode.GetDisplayNode(); displayNode.AutoWindowLevelOff(); displayNode.SetWindow(1400); displayNode.SetLevel(-500)" \
--point F.fcsv

Any idea what I need to change to get things working?

Also, I would eventually like to extend this code to also open the volume (DICOM series) to a specific index slice. I found the following code at this link:

layoutManager = slicer.app.layoutManager()
red = layoutManager.sliceWidget('Red')
redLogic = red.sliceLogic()
# Print current slice offset position
print(redLogic.GetSliceOffset())
# Change slice position
redLogic.SetSliceOffset(20)

Is this the correct code to modify to specify a slice for the Slicer GUI to open at?

2

I ended up figuring things out, here is what I did, in case it is of use for others…

Basically I was not “getting” the node correctly. Once I did, things worked properly. The code below will open the NRRD volume (200056.nrrd), change to lung windows (1400, -500), navigate to the index slice based on physical space, and add the fiducials.

To convert from slice number to physical space (offset), I took the RAS origin for inferior/superior axis which was -303.15, and “added” the distance to the index slice (index slice number (108) multiplied by the slice thickness (2.0 mm)). The fiducial file was previously saved from a Slicer session whereby I added two fiducials to arbitrary locations for testing purposes.

/Applications/Slicer\ 2.app/Contents/MacOS/Slicer --python-code "volumeNode = slicer.util.loadVolume('200056.nrrd', returnNode=True); volumeNode = getNode('200056'); displayNode = volumeNode.GetDisplayNode(); displayNode.AutoWindowLevelOff(); displayNode.SetWindow(1400); displayNode.SetLevel(-500); layoutManager = slicer.app.layoutManager(); red = layoutManager.sliceWidget('Red'); redLogic = red.sliceLogic(); redLogic.SetSliceOffset(-87.150)" --pointfile F.fcsv

The above code was ran in a bash shell on Mac OS.

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3

You can jump all slice views to a specific physical location using this code snippet:

slicer.modules.markups.logic().JumpSlicesToLocation(mean_Ras[0], mean_Ras[1], mean_Ras[2], True)

See complete example here: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_centroid_of_a_segment_in_world_.28RAS.29_coordinates

See examples of conversion between volume voxel and physical coordinates here: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_markup_fiducial_RAS_coordinates_from_volume_voxel_coordinates

4

Thanks for the response, @lassoan. Is it also possible to open a CT axial view (red) to a location based on the slice number/index, rather than the physical location? For example, open the CT to slice 108, rather than -85.150mm.

Something like this code:

redLogic.SetSliceOffset(-87.150)

But for slice number, rather than offset from the origin.

5

For most images that are read from DICOM, slices are stacked along the third (K) axis, so “slice number” (more accurately, InstanceNumber (0020,0013)) is often (K + 1) but it can be also (number of slices - K) or something else, because when DICOM readers reconstruct a volume, they don’t keep track of slice numbers and they may flip and interpolate slices (if they are not equally spaced) as needed.

If you need a robust mechanism to find closest slice index corresponding to a position, then you need to read ImagePositionPatient and ImageOrientationPatient tags for all the slices of the image, find the closest slice, and then get InstanceNumber of that slice.

Show DICOM slice number comes up time-to-time as a feature request, so if you implement this mechanism then it would be great if you could contribute it.

6

Also, FYI, if you load your images via the DICOM module as scalar volumes the DICOM.instanceUIDs attribute of the MRML node will have a list of SOPInstanceUIDs in slice order (the k dimension of IJK) so you can use that to look up the InstanceNumber.

Here’s some code that uses the dicom information for display (this could be extended to show the instance number in the case where the slice orientation corresponds to the acquisition plane)

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