Proposed revised atlas construction workflow - Revision history

Fedorov: /* Workflow / Tools */

2009-10-07T21:17:37Z

Workflow / Tools

Fedorov: /* Data */

2009-10-05T18:50:28Z

Data

Fedorov at 18:49, 5 October 2009

2009-10-05T18:49:52Z

Fedorov: /* Standing questions */

2009-10-05T18:46:50Z

Standing questions

Fedorov: /* Workflow / Tools */

2009-10-05T18:46:30Z

Workflow / Tools

Fedorov: /* Workflow / Tools */

2009-10-05T18:45:37Z

Workflow / Tools

Fedorov: /* Workflow / Tools */

2009-10-05T18:33:53Z

Workflow / Tools

Fedorov: /* References */

2009-10-05T18:23:06Z

References

Fedorov: /* References */

2009-10-05T18:22:58Z

References

Fedorov: Created page with '== Objective == Develop an atlas construction workflow for vervet segmentation, which will maximally (completely) consist of the NA-MIC tools. Learn from the previous experience…'

2009-10-05T18:21:37Z

Created page with '== Objective == Develop an atlas construction workflow for vervet segmentation, which will maximally (completely) consist of the NA-MIC tools. Learn from the previous experience…'

New page

== Objective ==

Develop an atlas construction workflow for vervet segmentation, which will maximally (completely) consist of the NA-MIC tools. Learn from the previous experience and try to mimic as closely as possible the workflow developed by Styner et al. [1]

== Workflow / Tools ==

{| class="wikitable" style="text-align:center; width:800px; height:200px" border="1"
|-
! Workflow step !! Description !! Tools
|-
! 1. Preparation
|
1.1. Select randomly a template image subject

1.2. Semi-automatically identify the ICC in the template subject.

1.3. 6+9+12 DOF registration of each of the subjects to the template.

1.4. Skull-strip each subject using dilated ICC of the template.

1.5. Perform intensity calibration to the template.

1.6. Use affine-registered, skull-stripped images to form initial affine average image.
||
1.1. n/a

1.2. Slicer Editor module

1.3. Slicer BRAINSFit extension

1.4. Slicer Mask, Editor modules (verify the mask encloses actual ICC!)

1.5. Slicer Histogram Matching module

1.6. ''Tool to be developed''
|-
! 2. Atlas construction
|

2.1. Use the affine registered image from Step 1.6 as the template to repeat Steps 1.1-1.6.

2.2. Perform non-rigid alignment of the subjects affinely registered to the template.

2.3. Compute the atlas as the average.

||
2.1 see above

2.2. Slicer BRAINSFit extension (BSpline), possibly Groupwise BSpline registration by Balci et al. [2]

2.3. Tool from step 1.6.

|-
! 3. Probabilistic atlas construction
|

3.1. Segment WM/GM/CSF from the averaged template, manually edit to ensure accuracy

3.2. Slightly smooth the segmentations Styner et al. recommend kernel of 0.4 mm variance.

3.3. Back-propagate WM/GM/CSF segmentations to the training subjects using the deformation field from Step 2.2.

3.4. Construct the probabilistic atlas by averaging of the tissue maps, normalize locally to 1, construct rejection class by inverting the sum of WM+GM+CSF.

|

3.1. Slicer editor module (thresholding, manual editing)

3.2. Gaussian smoothing module (check availability)

3.3. Slicer applyDeformation module (command line accessible only!)

3.4. Tool from Step 1.6, Slicer Editor module

|}

== Standing questions ==

* when to perform bias correction? After Step 1.4?
* deep brain structures -- similar approach for identification in subjects as for GM/WM/CSF in Step 3.1?

== References ==

# M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]

@@ Line 5: / Line 5: @@
 == Data ==
-vervet subjects (2 possibly unacceptable image quality), T1 sequence
+vervet subjects (2 subjects possibly have unacceptable image quality), T1 sequence
 == Workflow / Tools ==

← Older revision		Revision as of 18:23, 5 October 2009
Line 84:		Line 84:

	# M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]		# M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]
−
	# Balci S.K., Golland P., Wells W.M. Non-rigid Groupwise Registration using B-Spline Deformation Model. Insight Journal - 2007 MICCAI Open Science Workshop. [http://hdl.handle.net/1926/568 link]		# Balci S.K., Golland P., Wells W.M. Non-rigid Groupwise Registration using B-Spline Deformation Model. Insight Journal - 2007 MICCAI Open Science Workshop. [http://hdl.handle.net/1926/568 link]

← Older revision		Revision as of 18:22, 5 October 2009
Line 84:		Line 84:

	# M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]		# M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]
		+
		+	# Balci S.K., Golland P., Wells W.M. Non-rigid Groupwise Registration using B-Spline Deformation Model. Insight Journal - 2007 MICCAI Open Science Workshop. [http://hdl.handle.net/1926/568 link]

@@ Line 15: / Line 15: @@
 ! 1. Preparation
+|
 .1. Select randomly a template image subject
@@ Line 27: / Line 30: @@
 .6. Use affine-registered, skull-stripped images to form initial affine average image.
 ||
 .1. n/a

@@ Line 2: / Line 2: @@
 Develop an atlas construction workflow for vervet segmentation, which will maximally (completely) consist of the NA-MIC tools. Learn from the previous experience and try to mimic as closely as possible the workflow developed by Styner et al. [1]
 == Workflow / Tools ==
@@ Line 85: / Line 89: @@
 # M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf]
 # Balci S.K., Golland P., Wells W.M. Non-rigid Groupwise Registration using B-Spline Deformation Model. Insight Journal - 2007 MICCAI Open Science Workshop. [http://hdl.handle.net/1926/568 link]

@@ Line 79: / Line 79: @@
 * when to perform bias correction? After Step 1.4?
 * deep brain structures -- similar approach for identification in subjects as for GM/WM/CSF in Step 3.1?
+* Styner et al. used T2 to segment CSF. We only have T1
 == References ==

@@ Line 33: / Line 33: @@
 .5. Slicer Histogram Matching module
-.6. ''Tool to be developed''
+.6. ''Tool to be developed'': compute average image from the set of input images
 |-
 ! 2. Atlas construction

@@ Line 25: / Line 25: @@
 .1. n/a
-.2. Slicer Editor module
+.2. Slicer Editor module, SkullStripper Slicer module
 .3. Slicer BRAINSFit extension

@@ Line 71: / Line 71: @@
 .3. Slicer applyDeformation module (command line accessible only!)
-.4. Tool from Step 1.6, Slicer Editor module
+.4. Tool from Step 1.6, tool to be developed, Slicer Editor module
 |}