# Specialized Projects Menu

Specialized projects contains functions developed for a specific project and are not meant for general use. Therefore, only a brief description is provided.

## Contents

- 1 Functions
- 1.1 Dominate Non-Dominate Calculation
- 1.2 Multi Channel Mag/Phase Reconstruction
- 1.3 Integral Statistics
- 1.4 Vessel Tracking
- 1.5 Retina Test
- 1.6 Fourier Transform to RAW data
- 1.7 Reslice Coronal
- 1.8 Reslices Sagittal
- 1.9 Plot specific points or a circle
- 1.10 Old file converters
- 1.11 Find centerline and plot perpendicular distance
- 1.12 Caudate Segmentation
- 1.13 2D Caudate Segmentation
- 1.14 Tensor Based Registration
- 1.15 Diffusion Statistics
- 1.16 Save Objects as List
- 1.17 Simulate Half Ring
- 1.18 Save Single Echo
- 1.19 Convert DTI Maps to DICOM

## Functions

### Dominate Non-Dominate Calculation

Use Unknown

### Multi Channel Mag/Phase Reconstruction

Multi-Channel reconstruction algorithm for both magnitude and phase. Reconstructs images from multiple channels into a single image.

### Integral Statistics

Calculates the probability for a given signal, noise (sigma), and phase angle.

### Vessel Tracking

Old vessel tracking algorithm, based on a dynamic thresholding algorithm. **Deprecated**, use vascular tracking instead.

### Retina Test

Use unknown

### Fourier Transform to RAW data

Performs a Fourier transform to reconstruct k-space data from magnitude and phase images.

### Reslice Coronal

Reslices an axial dataset to coronal orientation. **Deprecated**, use multi-view reformat image instead.

### Reslices Sagittal

Reslices an axial dataset to sagittal orientation. **Deprecated**, use multi-view reformat image instead.

### Plot specific points or a circle

Use unknown

### Old file converters

Various programs to renumber, resort, and convert files. All file types should now be supported from File->Open, and conversions done with 'Save As...'

### Find centerline and plot perpendicular distance

Use unknown, **unstable crashes**

### Caudate Segmentation

Algorithm to segment the Caudate. Algorithm unknown.

### 2D Caudate Segmentation

Algorithm to segment the Caudate. Algorithm unknown.

### Tensor Based Registration

Algorithm Under Progress. Registration is employed in order to determine a pixel-to-pixel mapping between images of different modalities (co-registration), or between images of the same modality (registration).

Set of Operations that can be done using the module:

- Shifting of 2D and 3D images in X, Y, and, Z directions by user defined values
- Rotation of 2D images by user defined angles
- Rotation of 3D images around X, Y and Z axes by user defined angles
- Registration of two images

### Diffusion Statistics

Calculates statistics for a single ROI in 8 diffusion files and saves the results to an Excel spread sheet. By default, images are zoomed with the Fourier zoom, with a Hanning filter applied raised to the power specified ("Zoom Filter").

- Select all 8 diffusion files, and Excel output.
- Select the file to define the ROI on by pushing the "Open" button and selecting the appropriate file.
- Zoom the file to the same zoom factor that you selected
- Draw a boundary to define the ROI
- Select process

### Save Objects as List

Saves objects as a .GTR file, this is a simplified file format to be more easily read by other programs.

### Simulate Half Ring

Use unknown, **unstable crashes**

### Save Single Echo

Saves a single echo from the open dataset as the file name specified.

### Convert DTI Maps to DICOM

Converts a RAW DTI file (from DTI studio) to DICOM. DICOM header is copied from the original DICOM files used the generate the DTI maps.