Exporting markups data as a csv

Support
1

I’m having issues exporting data as a csv, I created all the markups and nodes I wanted to collected and couldn’t seem to export any of the data as a csv successfully. I would often get csv’s with random numbers or incomplete cells. I also am using two separate modules (Biomech and Morph) to collect volume data and general length data so I also wanted to know if there was an easier way to export all of the data onto 1 csv?

Thanks! :3

2

Did you try the Markup modules import/export tab? It allows you export the markups as a table inside slicer, which then you can save as a csv file.
Also you can copy and paste control points from the control points table to Excel.

That doesn’t sound right. How are you exporting these CSV files?

You can use the MergeMarkup module in SlicerMorph to merge all your markup nodes into a single markup object, which then you can use the export mechanism to save it as a csv file (or copy/paste to excel)

3

Hello!

Thank you for your help, I was able to export the data but instead of the Description (like the name of the line and the length/angle etc.) I only get the points back from Slicer.

I was wondering if there is a way to get the Descriptions for the nodes from Slicer instead of the points.

4

It is not clear what method you used to export the csv file from Markups. For me, if I use the import/export option in the Markups module, descriptions are correctly included. See the control points, and compare to the export csv file:

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5

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So here is what my Markup looks like, I was wondering if there was a way to get the names of the Nodes and Descriptions.

Thank you so much and sorry for any confusion, no one else in our lab knows how to use Slicer and we are all self-taught

6

And then here is the CSV that I can get from the all the merged markups.

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7

So that description in your first screenshot comes from measurement. But the description field in the exported csv file comes from the description field of the individual control points (highlighted in the red). If you entered something there in your original markups, the exported csv should have description field also populated.

I am not sure if there is a way to include the description field from the markup object (the one highlighted in blue). It is confusing that both of them are called description, but they are not the same things.

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