How to export list of selected volumes?

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How to export list of selected volumes?

Alexander Izvorski
Hello, 

I would like some way to select / mark 3D volumes in a 3D dicom file, and then save the list of 3D volumes to a file. The volume could be a rectangular box (by drawing box in two different views) or a sphere (by placing center marker and then selecting the size). The output file format can be anything, for example csv or xml.  I would like to have the marked volume coordinates in thefile, along with perhaps a custom name or some notes.

Slicer can open and display the files I'm working with just fine.  I looked around and found the "Create-and-place ROI" which creates a rectangular box, and I can see the list of ROIs under "Annotations", but I can't figure out a way to export this to file.  I'm using Slicer 4.6.2 on Linux.

Is ROI the right tool to use for this?  How to save them to file?

Thanks,
Alex


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Re: How to export list of selected volumes?

Andras Lasso-2

For rectangular ROI, you can use annotation ROI node. For circular ROI, you can use this script: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Manipulating_objects_in_the_slice_viewer (see other options in this thread: http://slicer-devel.65872.n3.nabble.com/Drawing-Circular-ROI-td4031087.html).

 

ROI position and radius is written to a simple csv-like file (.acsv) for each ROI. To get a single file with all the ROI data, probably the simplest is to write a small Python script that iterates through the ROIs and writes their data to file.

 

If you don’t want to write any program and you can use labelmaps as ROIs then you can use the Segment editor module to define arbitrarily shaped ROIs (for example, using the brush or scissors effect).

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Alexander Izvorski
Sent: March 5, 2017 3:22
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] How to export list of selected volumes?

 

Hello, 

 

I would like some way to select / mark 3D volumes in a 3D dicom file, and then save the list of 3D volumes to a file. The volume could be a rectangular box (by drawing box in two different views) or a sphere (by placing center marker and then selecting the size). The output file format can be anything, for example csv or xml.  I would like to have the marked volume coordinates in thefile, along with perhaps a custom name or some notes.

Slicer can open and display the files I'm working with just fine.  I looked around and found the "Create-and-place ROI" which creates a rectangular box, and I can see the list of ROIs under "Annotations", but I can't figure out a way to export this to file.  I'm using Slicer 4.6.2 on Linux.

 

Is ROI the right tool to use for this?  How to save them to file?

 

Thanks,

Alex

 


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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ