Importing a CT image stack into 3DSlicer 4.6.2

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Importing a CT image stack into 3DSlicer 4.6.2

N. MacLeod
Hello:

I’m just getting started with 3DSlicer 4 and this is probably a simple (boring) question. But here goes. I have a simple stack of tiff images from a CT scan of a cheetah skull and would like to use 3DSlicer to create a simple 3D scan that can be output in a standard 3d file format (e.g., STL). I’ve been through the 3DSlicer tutorials and the demonstration datasets appear to work a treat for this. However, none of those datasets appears to be a simple image stack. I can read the stack into 3DSlicer using the Data Load tool. But the software isn’t reformulating stack to reflect variation down the three spatial axes properly. I’ve been using ImageJ for this - so I know the stack can produce such a scan - but I’m not happy with the results I’m getting over there. 3DSlicer seems like a better tool for the job. I’ve also been though the support system and have found posts explaining how stacks can be imported in 3DSlicer 3. But the 3DSlicer 4 Data Load dialogs appears to differ from that previous version.  I’ve also read over the version 4 user’s guide and that’s not been much help either.

I’m sure there’s a simple way to do this. But I just haven’t stumbled across it. Does anyone know how to import a tiff image stack into 3DSlicer 4? Please send a link or set of instructions.

Thank you in advance.

With kind regards.

Norm MacLeod

_____________________________________________________

Professor Norman MacLeod
The Natural History Museum, Cromwell Road, London, SW7 5BD
(0)207 942-5204 (Office Landline)
(0)785 017-1787 (Mobile)
http://paleonet.org/MacLeod/

Department of Earth Sciences, University College
London, Gower Street, London WC1E 6BT, UK

Nanjing Institute of Geology & Palaeontology,
Chinese Academy of Sciences, 39 Beijing, Donglu, Nanjing, China
_____________________________________________________








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Re: Importing a CT image stack into 3DSlicer 4.6.2

Sharp, Gregory C.
Hi Norm,

If I understand your question, you wish to manually tweak the
voxel spacing (which is not correctly saved in your tiff stack).
Go to the "Volumes" Module.  Then, adjust "Image Spacing" settings.

Greg


-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of N. MacLeod
Sent: Thursday, March 30, 2017 2:22 AM
To: SPL Slicer Users
Subject: [slicer-users] Importing a CT image stack into 3DSlicer 4.6.2

Hello:

I’m just getting started with 3DSlicer 4 and this is probably a simple (boring) question. But here goes. I have a simple stack of tiff images from a CT scan of a cheetah skull and would like to use 3DSlicer to create a simple 3D scan that can be output in a standard 3d file format (e.g., STL). I’ve been through the 3DSlicer tutorials and the demonstration datasets appear to work a treat for this. However, none of those datasets appears to be a simple image stack. I can read the stack into 3DSlicer using the Data Load tool. But the software isn’t reformulating stack to reflect variation down the three spatial axes properly. I’ve been using ImageJ for this - so I know the stack can produce such a scan - but I’m not happy with the results I’m getting over there. 3DSlicer seems like a better tool for the job. I’ve also been though the support system and have found posts explaining how stacks can be imported in 3DSlicer 3. But the 3DSlicer 4 Data Load dialogs appears to differ from that previous version.  I’ve also read over the version 4 user’s guide and that’s not been much help either.

I’m sure there’s a simple way to do this. But I just haven’t stumbled across it. Does anyone know how to import a tiff image stack into 3DSlicer 4? Please send a link or set of instructions.

Thank you in advance.

With kind regards.

Norm MacLeod

_____________________________________________________

Professor Norman MacLeod
The Natural History Museum, Cromwell Road, London, SW7 5BD
(0)207 942-5204 (Office Landline)
(0)785 017-1787 (Mobile)
http://paleonet.org/MacLeod/

Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, UK

Nanjing Institute of Geology & Palaeontology, Chinese Academy of Sciences, 39 Beijing, Donglu, Nanjing, China _____________________________________________________








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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ