Modules:ARCTIC-Documentation-3.6 - Revision history

Cvachet: /* References */

2010-08-26T20:06:34Z

References

Cvachet: /* Quick Tour of Features and Use */

2010-04-06T21:48:39Z

Quick Tour of Features and Use

Cvachet: /* Quick Tour of Features and Use */

2010-04-06T21:36:16Z

Quick Tour of Features and Use

Cvachet: /* Quick Tour of Features and Use */

2010-04-06T21:31:26Z

Quick Tour of Features and Use

Cvachet: /* Tests */

2010-04-06T18:22:35Z

Tests

Cvachet: /* Source code & documentation */

2010-04-06T18:20:17Z

Source code & documentation

Cvachet: /* Dependencies */

2010-04-06T18:14:19Z

Dependencies

Cvachet: /* Tutorials */

2010-04-06T18:13:49Z

Tutorials

Cvachet: /* Module Type & Category */

2010-04-01T16:23:26Z

Module Type & Category

Cvachet: /* Quick Tour of Features and Use */

2010-04-01T16:03:46Z

Quick Tour of Features and Use

← Older revision		Revision as of 20:06, 26 August 2010
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	===References===		===References===
−	~~Publications related~~ to ~~this module go here~~. ~~Links to pdfs would be useful~~.	+
		+	* H.C. Hazlett, C. Vachet, C. Mathieu, M. Styner, J. Piven, Use of the Slicer3 Toolkit to Produce Regional Cortical Thickness Measurement of Pediatric MRI Data, presented at the 8th Annual International Meeting for Autism Research (IMFAR) Chicago, IL 2009.
		+	* C. Mathieu, C. Vachet, H.C. Hazlett, G. Geric, J. Piven, and M. Styner, ARCTIC – Automatic Regional Cortical ThICkness Tool, UNC Radiology Research Day 2009 abstract

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+|
 [[Image:ARCTIC.png|thumb|280px|ARCTIC User Interface]]
-* '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
+* '''Inputs''': Two modes exist to select input images needed to perform the cortical thickness analysis
-** T1-weighted image: set input T1 image, if available
+** '''Input mode 1 - Raw Images:''' set input images representing the different modalities of the same subject
-** T2-weighted image: set input T2 image, if available
+*** ''T1-weighted image:'' set input T1 image, if available
-** PD-weighted image: set input PD image, if available
+*** ''T2-weighted image:'' set input T2 image, if available
-** Tissue segmentation atlas directory: set directory containing gray-scale atlas to perform the tissue segmentation
+*** ''PD-weighted image:'' set input PD image, if available
-** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)
+*** ''Tissue segmentation atlas directory:'' set directory containing gray-scale atlas to perform the tissue segmentation
+*** ''Segmentation atlas type (T1 or T2, default: T1):'' set segmentation atlas type (should match subject input image)
+** '''Input mode 2 - Segmented Images:''' set tissue segmentation label image with its related raw image
-* '''Input 2: Segmented Images''' set tissue segmentation label image with its related raw image
+*** ''Tissue segmentation image:'' set tissue segmentation label image
-** Tissue segmentation image: set tissue segmentation label image
+*** ''White matter label (default: 1):'' set tissue segmentation white matter label
-** White matter label (default: 1): set tissue segmentation white matter label
+*** ''Gray matter label (default: 2):'' set tissue segmentation gray matter label
-** Gray matter label (default: 2): set tissue segmentation gray matter label
+*** ''CSF label (default: 3):'' set tissue segmentation CSF label
-** CSF label (default: 3): set tissue segmentation CSF label
+*** ''Raw image:'' set its related raw image (needed to perform a lobar analysis, i.e to perform the atlas warping)
 * '''Output:'''
-** Cortical thickness on white matter boundary: set output image which represents cortical thickness measurement on the white matter boundary
+** ''Cortical thickness on white matter boundary:'' set output image which represents cortical thickness measurement on the white matter boundary
-** Cortical thickness on gray matter boundary: set output image which represents cortical thickness measurement on the gray matter boundary
+** ''Cortical thickness on gray matter boundary:'' set output image which represents cortical thickness measurement on the gray matter boundary
-** Cortical thickness results directory: set output directory to save cortical thickness measurements
+** ''Cortical thickness results directory:'' set output directory to save cortical thickness measurements
-** ID number: set ID number to set prefix of the output images
+** ''ID number:'' set ID number to set prefix of the output images
 * '''Parcellation:''' set parameters to perform a lobar analysis
 ** If a parcellation is already defined for the subject:
-*** Case parcellation image: set the parcellation image defined in the subject space coordinate
+*** ''Case parcellation image:'' set the parcellation image defined in the subject space coordinate
 ** If a parcellation needs to be defined (i.e atlas registration will be performed):
-*** Atlas parcellation image: set the atlas parcellation image
+*** ''Atlas parcellation image:'' set the atlas parcellation image
-*** Atlas image: set the grayscale atlas image
+*** ''Atlas image:'' set the grayscale atlas image
 [[Image:ARCTIC_AdvancedParams.png|thumb|280px|ARCTIC Advanced Parameters User Interface]]
 * '''Advanced tissue segmentation parameters'''
-** Filter options: specifies smoothing parameters prior to the segmentation
+** ''Filter options:'' specifies smoothing parameters prior to the segmentation
-** Priors: set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
+** ''Priors:'' set prior weights for priors defined in the atlas directory. Prior weights can be adjusted globally (e.g., if one class overwhelms the other it can be set a lower weight) through comma separated numbers.
-** Maximum bias degree: set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
+** ''Maximum bias degree:'' set bias correction polynomial degree to adjust the severity of the bias field in the image. Bias field correction can be disabled by setting it to zero.
-** Atlas warping parameters: enable/disable B-spline warping and set grid size per direction (number of control points).
+** ''Atlas warping parameters:'' enable/disable B-spline warping and set grid size per direction (number of control points).
 * '''Advanced skull-stripping parameters'''
-** Mask dilation (default: disabled): check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.
+** ''Mask dilation (default: disabled):'' check button to slightly dilate the mask. Useful if the tissue segmentation doesn't perfectly mask the brain.
 * '''Advanced cortical thickness parameters:'''
-** InterpOff (default: disabled): check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
+** ''InterpOff (default: disabled):'' check button to gather interpolated cortical thickness measurements in two additionnal csv files. The method computes sparse measurement by default.
-** Threshold (default: 1.8): set distance threshold (in mm) used to match the cortical thickness map with the parcellation
+** ''Threshold (default: 1.8):'' set distance threshold (in mm) used to match the cortical thickness map with the parcellation
 * '''Advanced atlas registration parameters:'''
-** Choose between different initialization methods : see registration pipeline discussion
+** ''Initialization:'' choose between different initialization methods (see registration pipeline discussion)
 |}

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-[[Image:ARCTIC_AdvancedParams.png|thumb|280px|User Interface]]
+[[Image:ARCTIC_AdvancedParams.png|thumb|280px|ARCTIC Advanced Parameters User Interface]]
 * '''Advanced tissue segmentation parameters'''
 ** Filter options: specifies smoothing parameters prior to the segmentation

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 {|
+|
 * '''Input 1 - Raw Images:''' set input images representing the different modalities of the same subject
 ** T1-weighted image: set input T1 image, if available
@@ Line 80: / Line 81: @@
 *** Atlas parcellation image: set the atlas parcellation image
 *** Atlas image: set the grayscale atlas image
 * '''Advanced tissue segmentation parameters'''
 ** Filter options: specifies smoothing parameters prior to the segmentation
@@ Line 102: / Line 103: @@
 ** Choose between different initialization methods : see registration pipeline discussion
 |}

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 ===Tests===
-On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
+On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:
 * MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]

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 ===Source code & documentation===
-Download release source code via svn:
+* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
-* svn co https://skylla.ia.unc.edu/NeuroLib/Release/ARCTIC
+* Download release source code via svn:
 == More Information ==

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 ** [[Modules:RegisterImages-Documentation-3.6|Register Images]]
 ** [[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|ResampleScalarVectorDWIVolume]]
-* Publicly available atlases:
+* Publicly available atlases on MIDAS:
 ** [http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas]
 ** [http://www.insight-journal.org/midas/item/view/2328 Adult atlas]

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 * Tutorial Dataset
 ** [http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download Example dataset]
 ===Quick Tour of Features and Use===

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 Type: CLI
-Category: Pipeline
+Category: Workflow
 ===Authors, Collaborators & Contact===