CCB.DualSurfaceProtocolApplicationSummary (r1.1 vs. r1.27)
Diffs

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.27 - 21 May 2008 - CraigSchwartz)

META TOPICPARENT DualSurfaceWarpProjectDefinitionV1x0

A summary of the applications used to implement the elastic warp protocol

Line: 10 to 10
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour No No
Topological Contour Averager FlatMapAverager averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No No
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No No CCB/ComputeSurfaceWarp No No
Changed:
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Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No No CCB/ApplyWarp No No
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Fluid Warping tool ApplyFlatMapWarp applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No No CCB/ApplyWarp No No

Inflate Cortical Surface InflateSurface map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done     No No No CCB/InflateSurface No No
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No No CCB/InflateContour No No
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No No N/A No No

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.26 - 24 Apr 2008 - RyanCabeen)

META TOPICPARENT DualSurfaceWarpProjectDefinitionV1x0

A summary of the applications used to implement the elastic warp protocol

Line: 8 to 8
Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS SVN Download
Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No need SWDL ID Yes Yes Yes CCB/FlattenSurface No Yes
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour No No
Changed:
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Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No No
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Topological Contour Averager FlatMapAverager averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No No

Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No No CCB/ComputeSurfaceWarp No No
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No No CCB/ApplyWarp No No
Inflate Cortical Surface InflateSurface map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done     No No No CCB/InflateSurface No No

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.25 - 08 Apr 2008 - CraigSchwartz)
Changed:
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META TOPICPARENT ElasticWarpProjectDefinitionV1x0?
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META TOPICPARENT DualSurfaceWarpProjectDefinitionV1x0

A summary of the applications used to implement the elastic warp protocol

Essential Steps

Line: 32 to 32

Elastic Warping protocol links

Changed:
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ElasticWarpProjectDefinitionV1x0?
The main page of the shape tools elastic warp protocol
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DualSurfaceWarpProjectDefinitionV1x0
The main page of the shape tools elastic warp protocol

Changed:
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META TOPICMOVED craig date="1193690519" from="CCB.FluidProtocolApplicationSummary" to="CCB.ElasticProtocolApplicationSummary"
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META TOPICMOVED craig date="1207686822" from="CCB.ElasticProtocolApplicationSummary" to="CCB.DualSurfaceProtocolApplicationSummary"

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.24 - 05 Feb 2008 - CraigSchwartz)

META TOPICPARENT ElasticWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Essential Steps

Changed:
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Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS Download
Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No need SWDL ID Yes Yes Yes CCB/FlattenSurface Yes
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour No
Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No No CCB/ComputeSurfaceWarp No
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No No CCB/ApplyWarp No
Inflate Cortical Surface InflateSurface map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done     No No No CCB/InflateSurface No
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No No CCB/InflateContour No
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No No N/A No
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added Yes No Yes CCB/InterpolateContour No
Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No No CCB/ContourTopologyChecker No
Blend flattened surfaces BlendFlatmap Blends a dual and non-dual surface (.rdd files) Done No needs testing No No No CCB/BlendFlatmap No
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Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS SVN Download
Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No need SWDL ID Yes Yes Yes CCB/FlattenSurface No Yes
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour No No
Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No No
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No No CCB/ComputeSurfaceWarp No No
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No No CCB/ApplyWarp No No
Inflate Cortical Surface InflateSurface map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done     No No No CCB/InflateSurface No No
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No No CCB/InflateContour No No
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No No N/A No No
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added Yes No Yes CCB/InterpolateContour No No
Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No No CCB/ContourTopologyChecker No No
Blend flattened surfaces BlendFlatmap Blends a dual and non-dual surface (.rdd files) Done No needs testing No No No CCB/BlendFlatmap No No

Supporting Steps

not all are needed

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.23 - 22 Jan 2008 - CraigSchwartz)

META TOPICPARENT ElasticWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 6 to 6
Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS Download
Changed:
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No   Yes Yes Yes CCB/FlattenSurface No
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No need SWDL ID Yes Yes Yes CCB/FlattenSurface Yes

Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour No
Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No No CCB/ComputeSurfaceWarp No

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.22 - 18 Jan 2008 - CraigSchwartz)

META TOPICPARENT ElasticWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 16 to 16
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No No N/A No
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added Yes No Yes CCB/InterpolateContour No
Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No No CCB/ContourTopologyChecker No
Changed:
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Blend flattened surfaces BlendFlatmap Blends a dual and non-dual surface (.rdd files) Done No needs review No No No not yet in CVS No
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Blend flattened surfaces BlendFlatmap Blends a dual and non-dual surface (.rdd files) Done No needs testing No No No CCB/BlendFlatmap No

Supporting Steps

not all are needed

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.21 - 17 Jan 2008 - CraigSchwartz)
Changed:
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META TOPICPARENT FluidWarpProjectDefinitionV1x0?
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META TOPICPARENT ElasticWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Essential Steps

Line: 32 to 32

Elastic Warping protocol links

Changed:
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FluidWarpProjectDefinitionV1x0?
The main page of the shape tools elastic warp protocol
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ElasticWarpProjectDefinitionV1x0?
The main page of the shape tools elastic warp protocol

META TOPICMOVED craig date="1193690519" from="CCB.FluidProtocolApplicationSummary" to="CCB.ElasticProtocolApplicationSummary"

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.20 - 16 Jan 2008 - CraigSchwartz)

META TOPICPARENT FluidWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 6 to 6
Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS Download
Changed:
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No works, needs minor interface Yes Yes Yes CCB/FlattenSurface  
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour  
Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No   CCB/FlatMapAverager  
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No   CCB/ComputeSurfaceWarp  
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No   CCB/ApplyWarp  
Inflate Cortical Surface InflateFlatmap map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done   Need Dual, could be faster No No   CCB/InflateSurface  
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No   CCB/InflateContour  
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No      
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added Yes No Yes CCB/InterpolateContour  
Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No   CCB/ContourTopologyChecker  
UIF Blend Tool   Blends two (dual) UIF and create UCF of final surface. Done              
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No   Yes Yes Yes CCB/FlattenSurface No
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour No
Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No No CCB/FlatMapAverager No
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No No CCB/ComputeSurfaceWarp No
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No No CCB/ApplyWarp No
Inflate Cortical Surface InflateSurface map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done     No No No CCB/InflateSurface No
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No No CCB/InflateContour No
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No No N/A No
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added Yes No Yes CCB/InterpolateContour No
Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No No CCB/ContourTopologyChecker No
Blend flattened surfaces BlendFlatmap Blends a dual and non-dual surface (.rdd files) Done No needs review No No No not yet in CVS No

Supporting Steps

not all are needed
Line: 24 to 24
Description Program Name Details Status User
tested 		Problems & Issues PipeModule TWiki Grid Download
Changed:
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  GetDualContour?                
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Uif Shape reader ShapeTools library ShapeTools reader to interpret a UIF as an octagonal mesh. Done            

Trim Flatmap TrimFlatmap? trims 257x257 flatmap to match the current 256x256 flatmap uifs. (may also read non-UIF 2d flattened surface format).              
Changed:
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ImageJ Plugin Read OBJ ImageJ plugin to read contour obj Done In Progress          
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ImageJ Plugin Read OBJ ImageJ plugin to read contour obj Done            

  EncodeShape java port of program FlattenObj.c, a.k.a. _rec131072_other_octants.c - Done   Probably not needed        
Deleted:
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ColorMap Translator   Translate the encoded coordinates in a color map UIF into an              
UIF Shape reader ShapeTools library ShapeTools reader to interpret a UIF as an octagonal mesh.              
New Data format ShapeTools library Data file format to replace the various UIF images with a single file.              
Flattened Shape Statistics FlatStatistics                

Elastic Warping protocol links


 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.19 - 15 Jan 2008 - CraigSchwartz)

META TOPICPARENT FluidWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 6 to 6
Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS Download
Changed:
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Draft Complete No works, needs minor interface No No   CCB/FlattenSurface  
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour? No No   CCB/MapContour  
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Done No works, needs minor interface Yes Yes Yes CCB/FlattenSurface  
Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour Yes Yes Yes CCB/MapContour  

Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No   CCB/FlatMapAverager  
Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No No   CCB/ComputeSurfaceWarp  
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No No   CCB/ApplyWarp  
Inflate Cortical Surface InflateFlatmap map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done   Need Dual, could be faster No No   CCB/InflateSurface  
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No   CCB/InflateContour  
Changed:
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Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No   N/A No      
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added No No   CCB/InterpolateContour  
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Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No can't loop , or do foreach N/A No      
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added Yes No Yes CCB/InterpolateContour  

Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No   CCB/ContourTopologyChecker  
Changed:
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UIF Blend Tool   Blends two (dual) UIF and create UCF of final surface.                
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UIF Blend Tool   Blends two (dual) UIF and create UCF of final surface. Done              

Supporting Steps

not all are needed

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.18 - 13 Nov 2007 - CraigSchwartz)

META TOPICPARENT FluidWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 16 to 16
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No   N/A No      
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added No No   CCB/InterpolateContour  
Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No   CCB/ContourTopologyChecker  
Added:
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UIF Blend Tool   Blends two (dual) UIF and create UCF of final surface.                

Supporting Steps

not all are needed

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.17 - 06 Nov 2007 - CraigSchwartz)

META TOPICPARENT FluidWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 15 to 15
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No No   CCB/InflateContour  
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No   N/A No      
InterpolateContour InterpolateContour resamples contour files (obj and ucf). Done No need pipeline UI added No No   CCB/InterpolateContour  
Changed:
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Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". In Progress No needs debugging No No   CCB/ContourTopologyChecker  
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Check if contours are contained in flatmap ContourTopologyChecker Determines which contour files are in the flatmap, and which will "fall off". Done No needs debugging No No   CCB/ContourTopologyChecker  

Supporting Steps

not all are needed

 <<O>>  Difference Topic DualSurfaceProtocolApplicationSummary (r1.16 - 06 Nov 2007 - CraigSchwartz)

META TOPICPARENT FluidWarpProjectDefinitionV1x0?

A summary of the applications used to implement the elastic warp protocol

Line: 6 to 6
Description Program Name Details Status Tested Problems & Issues PipeModule TWiki Grid CVS Download
Changed:
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Flatten Cortical Surface FlattenShape? Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Draft Complete No works, needs minor interface No No   CCB/FlattenSurface  
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Flatten Cortical Surface FlattenSurface Maps the vertices of the cortical surface to a 2D map, presently represented as a pair of UIF files. Draft Complete No works, needs minor interface No No   CCB/FlattenSurface  

Flatten Cortical Lines MapContour Maps a contour to a space according to a map defined by flatten cortical surface Done No change name to FlattenContour? No No   CCB/MapContour  
Topological Contour Averager FlatmapAverager? averages contours, accounting for a complex surface topology. Done No need minor UI added No No   CCB/FlatMapAverager  
Changed:
<
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Fluid Warp calculation tool ComputeSurfaceWarp given a set of flattend contours, and a flattened surface, calculates the warp field. In Progress No debug covariant code, add flatmap topology (!) No     CCB/ComputeSurfaceWarp  
Fluid Warping tool ApplySurfaceWarp? applies a warp field to a flattened cortical surface. In Progress No need flatmap topology added,(pending completion of f.map topology in surface warp). No     CCB/ApplyWarp  
Inflate Cortical Surface InflateFlatmap map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface. Done   Need Dual, could be faster No     CCB/InflateSurface  
Inflate cortical lines InflateContour invert the cortical line flattening Done No   No     CCB/InflateContour  
Fluid Warp Pipeline LONI Pipeline a Pipeline dataflow implementing the fluid warp protocol. Started No   N/A        
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