Image orientation

Telling amap which way round your images are

If the supplied data does not match the NifTI standard orientation (origin is the most ventral, posterior, left voxel), then the atlas can be reoriented to match:

  • --flip-x Flip the sample brain along the first dimension

  • --flip-y Flip the sample brain along the second dimension

  • --flip-z Flip the sample brain along the third dimension

  • --orientation The orientation of the sample brain coronal, saggitalor horizontal

If your data isn't in a standard (i.e. anatomical orientation), and needs to be rotated, you can use the --rotation flag What follows the --rotation flag, must be a string in the format xIyJzK, where x, y & z are the axes to rotate around, and I, J & K are the number of 90 degree rotations for the respective axes. The direction of the rotation is:

  • For a rotation around X, the rotation is from the Y axis to Z

  • For a rotation around Y, the rotation is from the X axis to Z

  • For a rotation around Z, the rotation is from the X axis to Y

For example:

  • x0y0z3 would rotate around the Z axis 90 degrees clockwise (i.e. 270 degrees anticlockwise)

  • x0y0z0 would not rotate the image (default)

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