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Re: [SCIRUN-USERS] seg3d segmentation export to SCIRun question

Chronological Thread 
  • From: Jess Tate <>
  • Cc:,
  • Subject: Re: [SCIRUN-USERS] seg3d segmentation export to SCIRun question
  • Date: Tue, 14 Jul 2015 19:40:59 -0600

Hi Mike,

To Export a Segmentation to SCIRun,  you will need to save the segmentation to disk, then use SCIRun to open and then do whatever it is you wanted.

When you are ready to export your segmentation, You can use the Export Segmentation tool (in the file menu) to save out the segmentation.  You will be ask to save it as multiple files or a single file.  As a single file, you cannot have overlapping regions, and seg3d will overwrite with the last layer.   You can choose the label value for each region too.  whether it is a single file or multiple, you should save it in the nrrd format

Once you have saved out your segmentation,  you can open it is SCIRun with the ReadField Module (choose one of the nrrd options).   After that you can manipulate/visualize it however you want.  If you are new to SCIRun, I would suggest checking out the Tutorials on the SCIRun website to help you get started.  You can email this scirun-users mailing list with questions.


On Jul 14, 2015, at 7:07 PM, Elizabeth Jurrus <> wrote:

Hi Mike,

Forwarding your question to our mailing list.  Can you tell us what version of SCIRun you're running?

- liz

-------- Forwarded Message --------
Subject: Contact CIBC Submission
Date: Tue, 14 Jul 2015 16:48:25 -0600
From: SCI Webmaster <>

Michael Pennock <>

Affiliation: Penn State College of Medicine

Re Software: SCIRun

Subject: Seg3d segmentation or layer export

Message: Dear Sci Run,

Hi, thanks for making great products! So I have created a layer in Seg3D (it has all the masks and features I want, etc., and is ready to be exported) that I want to export to SciRun. However, when I use the export segmentation feature to export it as a nrrd file to Sci Run- it does not open in Sci Run. I have the X11 feature required to run Sci Run, and I am using a 2011 MacBook running Yosemite 10.10. Could you send me instructions for exporting Seg3d segmentations and opening them in Sci Run? I am not sure what I am missing.


Mike P.

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