MIP/SWI Processing

From Spin Help
Jump to: navigation, search

MIP/SWI processing generates MIP (Maximum/Minimum Intensity Projection)in two ways:

MIPmenu.jpg
  • 1) Simple MIP
  • 2) MIP with phase multiplications (SWI Processing)
  • 3) 3D MIP
  • 4) MIP Over Series
  • 5) Auto MIP

By default SPIN selects the Simple MIP


Simple MIP

Algorithm

The simple MIP can produce MIP (Maximum Intensity Projection) and mIP (Minimum Intensity Projection) images
MIP is a visualization method for 3D data that projects, to the visualization plane, the voxels with maximum (or minimum) intensities that lie on the path of parallel rays traced through the 3D dataset. In other works, each pixel in the MIP image is the highest (or lowest) intensity of that same position in the images that were used to create the MIP.

Input

M(m)IP Input Dialog

MIPInput.JPG

Here in the above window, we can choose either Maximum Intensity Projection (MIP) or Minimum Intensity Projection (mIP) to produce at one particular time. But by default, MIP is selected by the SPIN.

M(m)IP Input Parameters:

  • Total number of images: the number of all slices user wants to operate MIP process
  • Process Entire Series: all slices in the series of selected first image will be processed and the total number will be automatically updated
  • Number of Slices for each M(m)IP: how many slices will be used to generate one MIP or mIP result,which is 4 by default
  • Slide Window step: the overlap slices between previous M(m)IP and next M(m)IP file.
    • For example: when number of slices for each M(m)IP is 4, slide Window Step is 2, starting slices number is 1, slices: 1,2,3,4 will generate first MIP file, then slices 3,4,5,6 will generate next MIP file.
    • If we change the Slide Window Step to 1, with other parameters kept, lices: 1,2,3,4 will generate first MIP file, then 2,3,4,5 will generate the next MIP file.
  • The result file name: MaxIP_imagename.dcm format for MIP and as MinIP_imagename.dcm format for mIP by default or it also allows the user to name the file at his interest. The resulted MIP or mIP file is of *.dcm format stored in the same folder as the Magnitude images.
  • Advanced:
    • Skip number: is the slice number increment for reading next slice, by default it is 0.
    • Dicom Series: will be right to DICOM header as the series number
    • Image Order Descend: if selected, the slices will be read from end to beginning.

M(m)IP Output

In this example, the left image is one input slice, and the right image is the output: MIP for the whole series. We can see the artery of the leg clearly demonstrates on the right image.

MIPOutput.JPG

SWI Processing

Algorithm

A phase mask sensitive to negative phase values with a linear (dashed line) and 4th power mapping (solid line)

The susceptibility weighted image is created by combining the magnitude and phase images. A negative mask can be created from the phase image by mapping all values above 0 radians to be 1 and linearly mapping values from -π to 0 radians to range from 0 to 1, respectively. To increase the effect of the mask a 4th power function is commonly used instead of a linear mapping from -π to 0. The magnitude image is then multiplied by this mask. In this way phase values above 0 radians have no effect and phase values below 0 radians darken the magnitude image.

SWI Input

SWIProcessingDialog.PNG

The input is the acquired magnitude and phase images (phase images can be filtered or unfiltered)

SWI Parameters

  • Phase Masking: Sets what type of phase mask will be used to enhance the magnitude contrast. A negative phase mask darkens areas of negative phase, a positive phase mask areas of positive phase, and both darkens both. It is usually desired to emphasize the veins, the phase images should be inspected to see if they have positive (bright) or negative (dark) phase. The default for Siemens and Bruker systems is positive.
  • High Pass Filter: Specifies the size of high pass filter to apply to the phase image. If the phase image is already filtered set to zero.
  • Phase Zero: Sets what value is considered zero radians in the phase image. Should be close to the mean value of a phase image.
  • Magnitude Image: First magnitude image in series to process.
  • Phase Image: First phase image in series to process.
  • Unwrap Phase: Not functional.
  • Number of Images: Number of images to process.
  • Number of slices for each M(m)IP: Number of slices to do the maximum (or minimum) intensity projection over.
  • Number of Phase Multiplications: Number of times to multiply the magnitude image by the phase mask. Recommended 4.
  • Slide Window Step: Sets the number of slices to advance before calculating the next MIP. If zero (default) will advance by the MIP size so there is no overlap between MIPs. If set to less than MIP size each MIP image will overlap by a certain amount.
  • MIP Prefix: Prefix to append to created MIP images.
  • HP Prefix: Prefix to append to created filtered phase images.
  • Skip: Number of images to advance by when reading in original magnitude and phase images. Can be set to 2 if magnitude and phase images are interleaved. Default 1.
  • DICOM Series: Sets the series number for generated DICOM images. Defualt 0.
  • Image Order Descend: If images are in descending order, select the last image and choose this option.
  • Output Mask Image: Saves the phase mask image (that is multiplied by the magnitude image).

SWI Output

3D MIP

Algorithm

3D MIP is to generate a movie, usually in avi or mpeg file format, of rotating a 3D dataset from different angle along z axle, giving user a perspective of a product shown. It can generate the MIP effect or isosurface or volume renderring effects. It is applied on contrast enhanced MRA data most of the time to demonstrate vessel shape. A prepossessing, like vessel tracking, TSM on veesles, or subtraction of different time points will enhance the results a lot.

Input

3D MIP Input Dialog

3dmip1.jpg

Here in the above window, we can choose 3D Maximum Intensity Projection (3D MIP) to produce movie of 3D dataset. But by default, MIP is selected by the SPIN.

3D MIP Input Parameters:

  • Input first file name: First dicom of image series.
  • Number of Slices to MIP: Number of slices used to generate one MIP.
  • Size of animation(10-2048): Size of image that is generated.
  • Number of images/frames(1-500): Number of images in each frame
  • Threshold: The threshold value given by user.
  • Angle change per frame(-90-90): The frame rotation angle.
  • Display style: There are several display style.
    • Isosurface: Display the overall structure of the volume.
    • MIP: All of the data slab show pixel that has max intensity.
    • Volume Render: It adds 3D dimension to the 2D image.
  • Isovalue: Parameter for Isosurface volume rendering.
  • Smooth original data: Filter smooth original data.
  • Only Display Largest Region: Display the regions among the image.
  • Smooth 3D mesh: Option for the Isosurface smooth 3D mesh.
  • Remove Small Regions: Remove images specified below certain size.
  • Add outline: The outline(transparent 3D box) is created outside the 3D image
  • Save Movie/Images As: The path of the output file.

3D MIP Output

The output images of the 3D MIP. These are the two image from the series of image generated from the 3D MIP .

3DMIPoutput.jpg

MIP Over Series

Algorithm

The MIP over Series is a visualization method for 3D data. The input is more than one series of dicom images set. It MIP the respective slice from each image series. It produce one set of MIP image from several sets of dicom.

MIPoverseries1.jpg

Input

MIP Over Series

Here in the above window, we can choose MIP Over Series to produce at one particular time. But by default, MIP is selected by the SPIN.

MIP Over Series:

  • MIP Series Input: Minimum two image series is added.
  • Remove: This is used to remove a image series from the MIP Series Input list.
  • Output Folder and Prefix: The address of location to have the output of MIP Over Series.

MIP Over Series Output

In this example, the input is the two image series, and the below image is a dicom from the series of image is the output: MIP Over Series for the whole series. The input can be two or more series of images.

OutputMIPseries2.png

Auto MIP

Algorithm

Automip.jpg

The Auto MIP is a visualization method for 3D data. The input of series of dynamic contrast enhanced MRA data. It consist of several 3D MRA data at different time points.

Input

Auto MIP Input Dialog

Here in the above window, we can choose Auto MIP to produce at one particular time. But by default, MIP is selected by the SPIN.

Auto MIP Input Parameters:

  • Select Parent Folder of Case: Input is the case folder of all these MRA data. It will find all the MRA data under this folder to MIP for each MRA data. It provides a quick way to view 3D MRA with time change.
  • Sequence Length: Total number of slices in the image directory
  • Slice Per MIP: how many slices will be used to generate one MIP or mIP result,which is 4 by default
  • Step Size : the overlap slices between previous M(m)IP and next M(m)IP file.
    • For example: when number of slices for each M(m)IP is 4, slide Window Step is 2, starting slices number is 1, slices: 1,2,3,4 will generate first MIP file, then slices 3,4,5,6 will generate next MIP file.
    • If we change the Slide Window Step to 1, with other parameters kept, lices: 1,2,3,4 will generate first MIP file, then 2,3,4,5 will generate the next MIP file.
  • Sequences Remaining:

Auto MIP Output





Location