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`

,`saggital`

or`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)