Question on using decimated model in VMTK plugin

You can choose which point/cell data array to use for coloring in Models module Scalars section.

Thanks @lassoan

In summary, from what I understand, I think the size of celldata array is not equal to the number of segments (a segment is the vessel that lies between two junctions or a junction and a free end) in the network. And this is the question that I have raised in vmtk mailing list.

For small model, I could visually check for the number of segments and size of cell array. Both were equal.

I could check the celldata array’s size for the large model but I am not sure how to get the number of segments.

I’ve checked and tou are right, cells are indeed segments between branching points. So, I can add a quantification result table for them very easily.

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I’ve implemented curve node export and properties computation for extracted networks. It’ll be available in tomorrow’s Slicer Preview Release.

Glad to know that . I hope the coloring would also work fine now using cell data.

Thanks a lot for your wonderful support.

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A post was merged into an existing topic: Issues running latest preview on macOS/Windows 10

I utilized module “VMTK” to compute the centerline of lung airways, which need a long time to run.In addition,the result is not good.The airway tree is out of order and the centerlines line incorrectly.

And I installed other versions,like 4.11.0(2020-06-24) which doesn’t have the function “Centerline Compute”, 4.11.0(2020-05-14) which doesn’t have the option “Curve tree root” and can’t create the airway tree,those versions all can’t draw the tree.

In recent Slicer-4.11 version we hugely improved the module and renamed to “Extract centerline” to make it more consistent with module naming conventions. It has built-in automatic decimation to make centerline extraction 10x-100x faster without impacting accuracy, can work directly with segmentation input, export curves, compute statistics, etc.

I just installed the version 4.11.0(2020-08-18),but it doesn’t have the module “centerline compute”, so how can I get the centerline?

In recent Slicer-4.11 version we hugely improved the module and renamed to “Extract centerline” to make it more consistent with module naming conventions.

Sorry,I am new here.I clicked the “Apply”,but it seemed that nothing has happened.I can’t find the centerline in the module “Data”,and the “Table_1” is empty,as well as “PlotSeries_1”.

And what confused me is that the input of the module “centerline metrics” is “centerline”,but my purpose is to compute the centerline,which is really strange.

From your screenshot is seems possible to me that you created an empty model node called Model_1 and did the processing on that. If so, then it’s no surprise that the output is empty. Choose “Airway Label” instead.

Use ‘Extract centerline’ to compute a centerline.

‘Centerline metrics’ is meant to plot the diameter distribution around an existing centerline.

Thank you! I have ran the ‘Extract centerline’ following the video on Youtube.But there is nothing in the result ‘Centerline curve’ .
Do you know why?

You’d be better off by manually placing the endpoints; avoid the furthest extreme points; and results are more predictable if you avoid extracting bifurcated centerlines.

Thank you! I have solved it,and I have a new question which is that I want to save the ‘centerline curve’ and the ‘Centerline quantification’,so how to achieve that?

Doesn’t File/Save offer to save anything ?

Oh,you are right! I’m already confused by the software.Thank you very much!

That’s why we are here to help. Let us know if you have any suggestions for making the software simpler or more intuitive.