# vtkMarching squares for dicom stack \[XA\]

**URL:** <https://discourse.slicer.org/t/vtkmarching-squares-for-dicom-stack-xa/21249>\
**Category:** Support\
**Created:** [December 28, 2021, 12:14pm UTC](https://discourse.slicer.org/t/vtkmarching-squares-for-dicom-stack-xa/21249 "2021-12-28T12:14:51Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![cfd\_payne](https://avatars.discourse-cdn.com/v4/letter/c/e68b1a/32.png) [@cfd\_payne](https://discourse.slicer.org/u/cfd_payne)\
**Post date:** [December 28, 2021, 12:14pm UTC](https://discourse.slicer.org/t/vtkmarching-squares-for-dicom-stack-xa/21249/1 "2021-12-28T12:14:51Z")

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@lassoan relative to our discussion on vtkForum around reconstructing set of 2d+t dicom files with modality=XA.

> **[vtkMarchingSquares for DICOM \*.dcm/png/bmp stack](https://discourse.vtk.org/t/vtkmarchingsquares-for-dicom-dcm-png-bmp-stack/7510)**
>
> @lassoan @dgobbi Continuing the discussion from Stack of PNG files to be rendered as 3D: I have a similar situation where the data seems 2D+t \[typically coronary angiograms\], i’m trying to understand “qualitative” flow pattern before and after...

I followed your tutorial on CTA-cardio, however the dicom i have is not trivial [for me atleast],

1. when i load the dicom directory and examine , following are the warning i get  

2. when trying to carry out the segmentation, the 3D reconstruction is indefinite long squeeze  

how do i progress from here, how to get the time transient information while reconstructing the geometry

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [December 28, 2021, 12:37pm UTC](https://discourse.slicer.org/t/vtkmarching-squares-for-dicom-stack-xa/21249/2 "2021-12-28T12:37:25Z")

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Probably the best is to use the items provided by the “Image sequence” reader. Select those items (and unselect the MultiVolume reader’s items) and load them. Instead of manually uncheck the MultiVolume item and check the Image sequence items, it may be easier to disable the MultiVolume plugin in the settings in the module panel on the left.

There is a warning about image spacing because XA images are acquired with perspective projection therefore there is no spacing (mm/pixel) value ethat would be valid for all visible structures. You can compute the spacing a specific plane by measuring the size of an object of known physical size and multiply the spacing value in Volumes module’s Information section.

What would you like to segment on the images and why? What is your overall goal? What metrics would you like to compute? Is there a journal paper that describes the kind of analysis that you are trying to reproduce?

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**Author:** ![cfd\_payne](https://avatars.discourse-cdn.com/v4/letter/c/e68b1a/32.png) [@cfd\_payne](https://discourse.slicer.org/u/cfd_payne)\
**Post date:** [December 28, 2021, 1:46pm UTC](https://discourse.slicer.org/t/vtkmarching-squares-for-dicom-stack-xa/21249/3 "2021-12-28T13:46:30Z")

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> [@lassoan](#):
>
> Probably the best is to use the items provided by the “Image sequence” reader. Select those items (and unselect the MultiVolume reader’s items) and load them. Instead of manually uncheck the MultiVolume item and check the Image sequence items, it may be easier to disable the MultiVolume plugin in the settings in the module panel on the left.

Tried this but in vain.

> [@lassoan](#):
>
> What would you like to segment on the images and why? What is your overall goal? What metrics would you like to compute? Is there a journal paper that describes the kind of analysis that you are trying to reproduce?

Motivation1: enablers like [ContourTriangulator](https://kitware.github.io/vtk-examples/site/Cxx/Modelling/ContourTriangulator/), [MarchingSquares](https://kitware.github.io/vtk-examples/site/Cxx/Modelling/MarchingSquares/) for image processing whose inputs start from PNG, [ImageGradient](https://kitware.github.io/vtk-examples/site/Cxx/VisualizationAlgorithms/ImageGradient/) , [EnhanceEdges] from mhd

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/6/c6ae5f8321ca5807a6f14ed9933a6675c1f4fa9b.jpeg)

Motivation2:- to reproduce “qualitative” flow behavior from dicom instead of vtk as described in the below example & or visualize around arteries before/after stent placement  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/d/6d89ea6ee274b68852df96539176a00071c0b9a1.png)

Haven’t put any thoughts beyond the above reads.