2011 Winter Project Week:longitudinal dti analysis - Revision history

Anuja: /* Key Partners */

2011-01-14T15:13:41Z

Key Partners

Anuja: /* Key Partners */

2011-01-14T14:28:57Z

Key Partners

Anuja: /* Key Partners */

2011-01-10T13:36:03Z

Key Partners

Anuja at 13:20, 10 January 2011

2011-01-10T13:20:53Z

Anuja at 13:20, 10 January 2011

2011-01-10T13:20:19Z

Anuja: /* References */

2011-01-10T12:53:06Z

References

Anuja at 12:51, 10 January 2011

2011-01-10T12:51:55Z

Anuja: /* Key Partners */

2011-01-10T12:50:51Z

Key Partners

Anuja at 12:48, 10 January 2011

2011-01-10T12:48:41Z

Anuja: Created page with '==Key Partners== * Utah: Anuja Sharma, Guido Gerig * UNC: Martin Styner (Core 1) * Iowa: Hans Johnson (HD Project) * UCLA: Jack Van Horn (TBI Project)

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 <h3>Progress</h3>
-We began with exploring the non rigid Group-wise registration tool using the B-Spline deformation model (Golland et al.) available within the NAMIC kit to come up with a DTI Atlas. We explored a variety of options within it including different levels of multi-resolution optimization, number of iterations and B-Spline grid sizes. The affine step was not working as expected probably because of some further tuning needed within the parameters. So we tried to use the results of manual affine registration using Slicer (shown above in the images) as a prior to the groupwise tool. We still have to tweak the parameters around to get fine results for the mean atlas and the transformation fields.
+We began with exploring the non rigid Group-wise registration tool using the B-Spline deformation model (Golland et al.) available within the NAMIC kit to come up with a DTI Atlas. We explored a variety of options within it including different levels of multi-resolution optimization, number of iterations and B-Spline grid sizes. The affine step was not working as expected probably because of some further tuning needed within the parameters. So we tried to use the results of manual affine registration using Slicer as a prior to the groupwise tool. We still have to tweak the parameters around to get fine results for the mean atlas and the transformation fields.
 As another alternative, we are exploring the use of the DTI registration capability of Slicer. We found that once we get the transformed DTI images, we have tools to get the average DTI atlas for doing tractography. The required piece of interface here is a tool to use the deformation fields (corresponding to each transform between the individual image and the atlas) to map the tract back to individual subjects. Once we have the along tract information from each timepoint, we can use the DTI Tract Statistics tool to further statistically explore the localized variation of diffusion due to pathology or injury.
 Similarly, if we register the scalar images using Slicer, we need a tool which would provide the deformation fields (forward and backward mapping between individual subjects and atlas). The remaining steps could be done using tools developed by Casey Goodlet et al.
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 <h3>Progress</h3>
-We are currently exploring the Group-wise registration tool (Golland et al.) available within the NAMIC kit to come up with a DTI Atlas. We would also explore the projects 'DTI Registration and Resampling wizard' and 'DTI registration/processing pipeline in Slicer3' for more ideas and ease of access to tools needed for DTI Registration within Slicer.
+We began with exploring the non rigid Group-wise registration tool using the B-Spline deformation model (Golland et al.) available within the NAMIC kit to come up with a DTI Atlas. We explored a variety of options within it including different levels of multi-resolution optimization, number of iterations and B-Spline grid sizes. The affine step was not working as expected probably because of some further tuning needed within the parameters. So we tried to use the results of manual affine registration using Slicer (shown above in the images) as a prior to the groupwise tool. We still have to tweak the parameters around to get fine results for the mean atlas and the transformation fields.
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 <h3>Approach, Plan</h3>
-Begin with utilizing the existing DTI registration resources for co-registering the images from individual subjects (at varying timepoints: intra-subject). The input images would be scalars derived from the DWI/DTI inputs. For the specific scenarios of TBI and HD, different algorithms/parameter settings for registration would be compared. The aim is to build an atlas using the transformed images and getting transformation fields back to each timepoint image. This would be applied to deform the tensor field and finally come up with a DTI atlas.
+Begin with utilizing the existing DTI registration resources for co-registering the images from individual subjects (at varying timepoints: intra-subject). The input images would be scalars derived from the DWI/DTI inputs. For the specific scenarios of TBI and HD, different algorithms/parameter settings for registration would be compared. The aim is to build an atlas using the transformed images and getting transformation fields back to each timepoint image. This would be applied to deform the tensor fields and finally come up with a DTI atlas.
-Post successful DTI atlas building, we would proceed with tractography followed by arc-length parametrization along the fiber bundles and the use of existing DTI-statistical-analysis framework with along-tract kernel regression. The framework was originally developed by Casey Goodlett and has been modified and updated by the Utah and UNC groups.
+Post successful DTI atlas building, we would proceed with tractography in the DTI atlas image, transformed back again to get the same tract geometry from individual images. This is followed by arc-length parametrization along the fiber bundles and the use of existing DTI-statistical-analysis framework with along-tract kernel regression. The framework was originally developed by Casey Goodlett and has been modified and updated by the Utah and UNC groups.

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 <gallery>
 Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
-Image:namic.png|Longitudinal DTI Analysis for patient follow-up images- complete processing pipeline
+Image:longitudinal_dti.png|Longitudinal DTI Analysis for patient follow-up images- complete processing pipeline
 </gallery>

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 <gallery>
 Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
+Image:namic.png|Longitudinal DTI Analysis for patient follow-up images- complete processing pipeline
 </gallery>

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 ==References==
 * [http://www.na-mic.org/Wiki/index.php/Projects:GroupwiseRegistration Group-wise Registration]
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← Older revision		Revision as of 12:51, 10 January 2011
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		+	<gallery>
		+	Image:PW-SLC2011.png\|[[2011_Winter_Project_Week#Projects\|Projects List]]
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		+	</gallery>
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	==Key Partners==		==Key Partners==
	* Utah: Anuja Sharma, Guido Gerig		* Utah: Anuja Sharma, Guido Gerig

← Older revision		Revision as of 12:50, 10 January 2011
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	<div style="width: 97%; float: left;">		<div style="width: 97%; float: left;">
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		+	==References==
		+	* [http://www.na-mic.org/Wiki/index.php/Projects:GroupwiseRegistration Group-wise Registration]
		+	</div>