Is there a way to crop images with multiple objects per scan? Please help!

[rbas...@stanford.edu]

We imaged 4 fish brains in each scan and I'm trying to figure out if there is a simple way to create four separate files from this one scan. As of now I've been able to save the image after using the snake tool to get one of the brains in view and then reorienting the picture to be in the proper plane by going to registration and then manually tilting the image to get proper slices to show up. However, this only works with the original image also open and the cropped image added as another image, and I'm running into other problems when I try to segment.

Please help!

[Paul Yushkevich]

Hi

I am not sure if I am answering the right question, but when you go into snake mode, you can select a region of interest (ROI) for the automatic segmentation. If you want, once you enter snake mode you can save this ROI as a separate image (File->Save Main Image ROI), and open it as the main ITK-SNAP image later. 

Let me know if that's of any help

Paul

On Thu, Jun 29, 2017 at 11:42 PM, <rbas...@stanford.edu> wrote:

We imaged 4 fish brains in each scan and I'm trying to figure out if there is a simple way to create four separate files from this one scan. As of now I've been able to save the image after using the snake tool to get one of the brains in view and then reorienting the picture to be in the proper plane by going to registration and then manually tilting the image to get proper slices to show up. However, this only works with the original image also open and the cropped image added as another image, and I'm running into other problems when I try to segment.

Please help!

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[rbas...@stanford.edu]

Dear Paul,

This works fine initially, but my bigger problem lies in the orientation of the slices after cropping. Each brain needs to be manually tilted so that I can get the properly oriented slices to view and segment (since they weren't carefully oriented before scanning). So far the only way I've been able to reorient them properly has been (tools --> registration --> manual --> interactive tool) but it will only let me do the registration if I add the cropped image as another image rather than the main image and then I have to upload the transformation file to get the proper orientation. Is there a way to save the images in the proper orientation without having to upload the transformation file? Also, I haven't been able to find much information about what the purpose of the registration is/ how to use it, could you tell me a little about this or direct me to the proper place? ITK SNAP has also been crashing on me quite often as I try to tilt the image, and even more when I try to start segmenting the cropped and tilted image.

Thanks for all your help!
Roya

On Sunday, July 2, 2017 at 10:02:47 AM UTC-7, Paul Yushkevich wrote:

Hi

I am not sure if I am answering the right question, but when you go into snake mode, you can select a region of interest (ROI) for the automatic segmentation. If you want, once you enter snake mode you can save this ROI as a separate image (File->Save Main Image ROI), and open it as the main ITK-SNAP image later. 

Let me know if that's of any help

Paul

On Thu, Jun 29, 2017 at 11:42 PM, <rbas...@stanford.edu> wrote:

We imaged 4 fish brains in each scan and I'm trying to figure out if there is a simple way to create four separate files from this one scan. As of now I've been able to save the image after using the snake tool to get one of the brains in view and then reorienting the picture to be in the proper plane by going to registration and then manually tilting the image to get proper slices to show up. However, this only works with the original image also open and the cropped image added as another image, and I'm running into other problems when I try to segment.

Please help!

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