Documentation/Nightly/Modules/SwissSkullStripper - Revision history

Lasso at 13:00, 16 July 2019

2019-07-16T13:00:04Z

Lasso at 12:36, 16 July 2019

2019-07-16T12:36:54Z

Lasso at 12:35, 16 July 2019

2019-07-16T12:35:26Z

Lasso at 12:34, 16 July 2019

2019-07-16T12:34:52Z

Lorensen at 19:33, 13 September 2013

2013-09-13T19:33:43Z

Lorensen at 17:34, 16 June 2013

2013-06-16T17:34:12Z

Lorensen at 13:14, 16 June 2013

2013-06-16T13:14:17Z

Lorensen: Created page with '{{documentation/versioncheck}} {{documentation/{{documentation/version}}/module-header}}

@@ Line 28: / Line 28: @@
 the edge of the brain-skull border with dedicated expansion, curvature
 and advection terms.
 The module produces a brain mask for the patient data as well as the patient data with the mask applied.<br>
 For the atlas, a customized isotropic T1-weighted MR image and a manually generated brain mask are available for download.
-* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha Download the atlas image]
+Users can also provide their own atlas image and brain mask.
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@@ Line 56: / Line 51: @@
 |[[Image:SwissSkullStripperPanel.png|thumb|280px|Module UI]]
 |}
-The user provides three input volumes:
+# Load atlas image and atlas brain mask volumes:
-# An atlas image volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha download one].
+#* Option A: Go to ''Sample data'' module, scroll down to ''SwissSkullStripper'' category, and click on ''SwissSkullStripperAtlasImage'' and ''SwissSkullStripperAtlasMask'' images
-# An atlas brain mask volume, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].
+#* Option B: Use your own atlas image (or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha download one]) and corresponding atlas brain mask volume (or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one]). '''Important: in ''Add data'' dialog, click ''Show options'' and make sure ''Labelmap'' checkbox is checked for the for the brain mask volume''' (if this step is missed then the mask volume will not appear in the atlas mask volume selector)
-#* '''Important: in ''Add data'' dialog, click ''Show options'' and make sure ''Labelmap'' checkbox is checked for the mask''' (if this step is missed then the mask volume will not appear in the atlas mask volume selector)
+# Load a patient volume. Use your own, or ''MRBrainTumor1'' sample data or  [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/RegLib_C01_MRMeningioma_1.nrrd download one].
-# A patient volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/RegLib_C01_MRMeningioma_1.nrrd download one].
+# Go to ''Swiss Skull Stripper'' module
-The module produces:
+# Select ''Patient volume'' (e.g., ''MRBrainTumor1''), ''Atlas volume'' (e.g., ''atlasImage''), ''Atlas mask volume'' (e.g., ''atlasMask'')
-# A patient volume that resides within the patient mask
+# Create new volumes for ''Patient output volume'' and ''Patient mask label''
-# A patient brain mask volume
+# Click Apply. Within about 2 minutes, the module produces:
-The process takes about 2 minutes for most datasets.
+## A patient volume that resides within the patient mask
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 # An atlas image volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha download one].
 # An atlas brain mask volume, Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha download one].
 # A patient volume. Use your own, or [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/RegLib_C01_MRMeningioma_1.nrrd download one].
 The module produces:

@@ Line 34: / Line 34: @@
 * [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha Download the atlas image]
 * [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask]
-* Load the two image and mask files into Slicer using menu ''File'' / ''Add data'' or by drag-and-dropping the files to the application window. '''Important: in ''Add data''' dialog, click ''Show options'' and make sure ''Labelmap'' checkbox is checked for the mask''' (if this step is missed then the mask volume will not appear in the atlas mask volume selector)
+* Load the two image and mask files into Slicer using menu ''File'' / ''Add data'' or by drag-and-dropping the files to the application window.
 Users can also provide their own atlas image and brain mask.

@@ Line 27: / Line 27: @@
 brain extraction based on level-sets. The level-set is evolved towards
 the edge of the brain-skull border with dedicated expansion, curvature
-and advection terms.<br>
+and advection terms.
-The module produces a brain mask for the patient data as well as the patient data with the masj applied.<br>
 For the atlas, a customized isotropic T1-weighted MR image and a
-manually generated brain mask are available for download.
+The module produces a brain mask for the patient data as well as the patient data with the mask applied.<br>
 * [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha Download the atlas image]
-* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask] '''NOTE: After you load the atlas brain mask, go to ''Volumes'', set the ''Active Volume'' to atlasMask. Then open ''Volume Information'' and check ''LabelMap''.'''
+* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask]
-Users can also provide their own atlas image and brain mask. Be sure that the brain mask is loaded as a ''LabelMap''.
+* Load the two image and mask files into Slicer using menu ''File'' / ''Add data'' or by drag-and-dropping the files to the application window. '''Important: in ''Add data''' dialog, click ''Show options'' and make sure ''Labelmap'' checkbox is checked for the mask''' (if this step is missed then the mask volume will not appear in the atlas mask volume selector)
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 {{documentation/{{documentation/version}}/module-section|Use Cases}}

@@ Line 32: / Line 32: @@
 manually generated brain mask are available for download.
 * [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasImage.mha Download the atlas image]
-* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask]
+* [https://github.com/lorensen/SwissSkullStripperExtension/raw/master/SwissSkullStripper/Data/Input/atlasMask.mha Download the atlas brain mask] '''NOTE: After you load the atlas brain mask, go to ''Volumes'', set the ''Active Volume'' to atlasMask. Then open ''Volume Information'' and check ''LabelMap''.'''
-Users can also provide their own atlas image and brain mask.
+Users can also provide their own atlas image and brain mask. Be sure that the brain mask is loaded as a ''LabelMap''.
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 {{documentation/{{documentation/version}}/module-section|Use Cases}}