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[[http://www.slicer.org|3D Slicer]] is a software program for visualization, registration, segmentation, and quantification of medical data. It is developed as a collaboration between the MIT AI Lab and the Surgical Planning Lab at Brigham & Women's Hospital. The 3D Slicer homepage is [[http://www.slicer.org|http://www.slicer.org]]. [http://www.slicer.org 3D Slicer] is a software program for visualization, registration, segmentation, and quantification of medical data. It is developed as a collaboration between the MIT AI Lab and the Surgical Planning Lab at Brigham & Women's Hospital. The 3D Slicer homepage is [http://www.slicer.org http://www.slicer.org].
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Within the MGH NMR Center, 3D Slicer is already installed on the network for both the Linux and Mac OS (PowerPC and Intel) platforms. You start 3D Slicer v2.6, which is the current stable version, by typing: Within the MGH NMR Center, 3D Slicer is already installed on the network for both the Linux and Mac OS (PowerPC and Intel) platforms. You start 3D Slicer by typing:
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slicer2 slicer3
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 * 'slicer2' is a wrapper-script found in /usr/pubsw/bin, which starts the stable version 2.# of 3D Slicer for the platform you are using. Older and alpha versions of 3D Slicer are found in /usr/pubsw/packages/slicer. The one considered the most stable is found in /usr/pubsw/packages/slicer/current.
 * Beta version 3 of 3D Slicer is also available. This command is used to start it:
 * 'slicer3' is a wrapper-script found in /usr/pubsw/bin, which starts 3D Slicer for the platform you are using. Older and alpha versions of 3D Slicer are found in /usr/pubsw/packages/slicer. The one considered the most stable is found in /usr/pubsw/packages/slicer/current.
 * The old version 2 of 3D Slicer is also available. This command is used to start it:
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slicer3 slicer2
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If you want to install 3D Slicer on your non-networked computer, go to the [[http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started|Slicer2.6_Getting_Started]] page and follow the simple instructions for your machine. If you want to install 3D Slicer on your non-networked computer, go to the [http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer2.6_Getting_Started] page and follow the simple instructions for your machine.
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To learn more about using Slicer, refer to the [[http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101|Slicer_User_Training_101]] page which contains self-guided tutorials and sample data for Slicer2.6. Specifically, the [[http://www.na-mic.org/Wiki/images/4/4e/SlicerTraining6_vtkFreeSurferReaders.ppt|Slicer Training 6: vtkFreeSurferReaders Module tutorial]] will teach you how to visualize Freesurfer generated subcortical segmentations and cortical parcellations both as color coded shading and as 3D models (see screenshots below). To learn more about using Slicer, refer to the [http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer_User_Training_101] page which contains self-guided tutorials and sample data for Slicer2.6. Specifically, the [http://www.na-mic.org/Wiki/images/4/4e/SlicerTraining6_vtkFreeSurferReaders.ppt Slicer Training 6: vtkFreeSurferReaders Module tutorial] will teach you how to visualize Freesurfer generated subcortical segmentations and cortical parcellations both as color coded shading and as 3D models (see screenshots below).
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{{attachment:FreesurferSlicer1.jpg}} attachment:FreesurferSlicer1.jpg
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{{attachment:FreesurferSlicer2.jpg}} attachment:FreesurferSlicer2.jpg

3D Slicer

[http://www.slicer.org 3D Slicer] is a software program for visualization, registration, segmentation, and quantification of medical data. It is developed as a collaboration between the MIT AI Lab and the Surgical Planning Lab at Brigham & Women's Hospital. The 3D Slicer homepage is [http://www.slicer.org http://www.slicer.org].

MGH NMR Center Installation

Within the MGH NMR Center, 3D Slicer is already installed on the network for both the Linux and Mac OS (PowerPC and Intel) platforms. You start 3D Slicer by typing:

slicer3

Notes:

  • A command named 'slicer' exists in the FSL toolset, and is completely unrelated to the 3D Slicer application, so remember not to confuse the two.
  • 'slicer3' is a wrapper-script found in /usr/pubsw/bin, which starts 3D Slicer for the platform you are using. Older and alpha versions of 3D Slicer are found in /usr/pubsw/packages/slicer. The one considered the most stable is found in /usr/pubsw/packages/slicer/current.
  • The old version 2 of 3D Slicer is also available. This command is used to start it:

slicer2

Download

Remember that you do not need to install 3D Slicer if you are connected to the NMR Center network (see above).

If you want to install 3D Slicer on your non-networked computer, go to the [http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer2.6_Getting_Started] page and follow the simple instructions for your machine.

Usage

To learn more about using Slicer, refer to the [http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer_User_Training_101] page which contains self-guided tutorials and sample data for Slicer2.6. Specifically, the [http://www.na-mic.org/Wiki/images/4/4e/SlicerTraining6_vtkFreeSurferReaders.ppt Slicer Training 6: vtkFreeSurferReaders Module tutorial] will teach you how to visualize Freesurfer generated subcortical segmentations and cortical parcellations both as color coded shading and as 3D models (see screenshots below).

Work Flows

See the SlicerWorkFlows page.

Screenshots

Below are screenshots of 3D Slicer making use of the vtkFreeSurferReaders module to display subcortical segmentation (aseg.mgz) slices and selected structure volumes:

attachment:FreesurferSlicer1.jpg

Detail of the hippocampus:

attachment:FreesurferSlicer2.jpg

Slicer (last edited 2009-04-22 16:25:11 by NickSchmansky)