File Exchange > Data Analysis >    NIfTI Slicer

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This app can help neuroscientists to convert the 3d NIfTI file into sections.

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This app can help neuroscientists to convert the 3d NIfTI file into slices.


Download the opx file from this page and then drag and drop it onto the Origin workspace, or click the Add Apps button to open the App Center and then search for &ldquonifti&rdquo to download and install.

Note that this tool requires the Pro version.


Click on this app icon, and a small toolbar will appear in the center of Origin workspace. There are three buttons on the toolbar:

1. Import NIfTI File: import the *.nii.gz file into an Image Window.

Click the Import NifTi File button to browse the folder and select *.nii.gz file:

  • Input File: the selected NifTI file
  • Plane: Specify an anatomical plane to display the view

Once you click the OK button, Origin will create an Image window that should contain all the frames of the selected files, and you can drag the slider to view the frames.

2. Apply LUT: apply color to the image window based on a color lookup table.

Before clicking the Apply LUT button to open a dialog, prepare the color value first. We have provided a color sample file in this App, you can right-click on the App icon and select Show in Folder, then drag the file LabelIndexMapper.ogwu directly into Origin directly.

Click Apply LUT button to specify the color columns and the Image window and get an RGB-colored Image:

  • Mapper: Specify one column for pixel and another for color hex code
  • Image: Specify the Image window to be colorized

3. Tilt and Rotate: tilt and rotate the image window generated by the imported NIfTI file to match the *.tif image

Click the Tile and Rotate button to open a dialog and preview the slice. There are 3 sliders to change the angles:

  • Z: Specify the Z-offset
  • Tilt: Tilt counterclockwise by the specified angle.
  • Rotate: Rotate counterclockwise on the Z-axis by the specified rotation angle
  • Missing Value: Set a user-defined missing value to specify transparent voxel

This dialog also provides a diagram showing the position of the plane on the left and a slice preview on the right.


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