• ApplyFlatMapWarp - uses a pre-computed warp field to warp a flattened surface

• FlatMapAverager - averages flattened contours

Dual Surface Warp Protocol Project Definition ( v1x01 )

Elastic Warp Protocol Project Definition ( v1x01 )

• InflateSurface - maps a flattened surface into a three dimensional surface.

Warp Protocol diagram

Process Flow

• FlattenSurface - maps an OBJ to a (uif) flatmap.

• Notes on the Original fluid warp protocol

• InflateContour - maps a flattened contour into a three dimensional contour.

Replacement Analysis Programs

• MapContour - flattens contours
• FlattenShape^? - maps an OBJ to a (uif) flatmap.
• FlatmapAverager^? - averages flattened contours
• ComputeSurfaceWarp - warps a flatmap according to contours.
• InflateContour - maps a flattened contour into a three dimensional contour.
• ApplySurfaceWarp^? - uses a pre-computed warp field to warp a flattened surface
• InflateFlatmap - maps a flattened surface into a three dimensional surface.
• getDual - gets the dual flatmap from a flatmap
• getDualContour - gets a contour, in the dual flatmap space.
• TrimFlatmap^? - trims the edges of a flat map.

Big Flat maps have duplicate points

The flatmap obtained from flattening the cortex obj. contains several regions of duplicate encoded points. That is, multiple pixels have the same color.

the program rec131072_other_octants only writes one eighth of the output image.

This program, run 8 times with the differing face definitions of the octants, always writes into the same region of it's output UIF. Thus, the 8 output files so generated will contain the same 1/8 region that is not black, although the colors will vary, as these encode the coordinates of the differing octants.

(program that assembles the 8 octants into a "BIG" image) may mishandle boundaries

Issues with current protocol

RSP Interpolation

Incorrect Flattened Contour Averaging ("lines fall off")

Annotated Current Scripts

A complete, annotated Fluid Warp Protocol

Applications Summary

A table summarizing the applications^?

Applications - Rough Notes

Notes on Averaging process

we found that the "lines fall off" fall off in the process of mapping the (sulcal) lines, drawn in the obj 3d space, onto the flat map. we speculate that the discarded lines are thrown away when a mapped vertex or face crosses more then one octant.

(note: octant,here, is misnomer, as each hemisphere is split into 8 portions, not the entire brain as we'd previously speculated).

The mapped lines are flat, that is, all have the same z coordinate.

the average, accomplished by the script

/data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/surfNstat3D

is probably a simple average of the coordinates, from which the "fallen" lines have previously been excluded.

called from script /cxfs/schizo/family_study/scripts/medial_analysis/09a_script_flat_av_medial_LandR.csh

• • a class to read LONI Uif files (RGB and FPIC) into a Shape, or a BufferedImage

The LHS sample script 07_Local_dual_med_flat_catchL.csh contains the commands currently used to flatten a hemisphere.

Notes on the flattening process are Here.

Project Plan

• • An ImageJ plugin (UifImageJ) that enables ImageJ to read Loni RGB and FPIC UIF files.
  • A topology aware averager.
• support classes
  • a class to read LONI Uif files (RGB and FPIC) into a Shape, or a BufferedImage^?

Data Samples

Data File Format notes

Analysis Protocol

ColorMap Translator

Fluid Warp Protocol Project Definition ( v1x01 )

Public Project Description - none yet available

Overview

Restrictions, Exclusions, Limitations

• Assumes that contour shapes use an IContourEdgeSet (except for UCF, which are handled as a special case)

People Affected

Version

Requirements

• Java 1.5 is used to implement the tools produced by this project.

Requirements Change Procedure

• Changes to be mutually agreed upon by CS and programmer.
• Changes and their date will be entered in a 'requirements change' list.

Requirements Changes

Products

This project will result in the following products:

• Applications
• Documentation
  • Various TWiki web pages including

Approach

discarded approach 1

(reasons why it was abandoned)

discarded approach 2

(reasons why it was abandoned)

Notes

Analysis Protocl

1. Brain Scan
2. Fit template (LHS) cortex to scan, output is an OBJ surface.
3. Manual deliniation of lines (sulci) , saved as OBJ lines.
4. Surface "flattened" into "diamond" ucf files.
5. Lines flattened into ucf files.
6. Perform Fluid warp using lines and surfaces.
7. Average lines to form population averages.
8. Inflate warped surfaces and lines back into 3d.

Applications

ColorMap^? Translator

Flatten Cortical Surface

• will need to optionally mimic the rounding of OBJ co-ordinates onto current "flat" ucf files.
• find how current code stores the 3d coordinates of the flattened vertices
  • uif "colormap" images may be an approximation
  • precise map may be elsewhere
• ability to translate between a vector field of point mappings

Inflate Cortical Surface

Using the flattening map created by the Flatten Cortical Surface program, apply the inverse transform to map the warped, flattened surfaces and lines to a 3 dimensional triangulated surface.

Flatten cortical lines

• • Will fix the "lines fall Off" problem
  • will need to find triangle whose face contains the line, find the affine trf. taking the three vertices of this triangle onto the flat space, then apply this map to the endpoints of the line. Will need to handle distortions caused by representting triangle (obj) as quads(diamond ucf).

Inflate cortical lines

Contour averager

• need tool to get neighbors of a vertex, that 'wraps" over the patches compromising the diamond surface' trianguls,

Fluid Warping tool

topology description

note we need to better understand how to solve the fluid warp.

RACI Chart

R - Responsible person
A - Actions taken (Authorizes something, provides support, et. cetera)
C - Communicates or consults with this person
I - Inform this person

Lessons Learned

• lesson 1
• lesson 2