orient_mri - graphically and interactively re-orient an MRI volume and save the new transform


orient_mri [--volume VOLUME_NAME [VOLUME_NAME...]]


Optional Flagged Arguments


Filename of a volume

The direct file name of a volume, e.g. an .mgz file, a file, or a .img file


This program provides an interactive way to change and save the orientation of an MRI volume (its "Voxel to RAS" transform). You can rotate the volume to a new orientation, check the cross sections, and save the transform. This program only modifies the rotation component of the RAS transform; it will not modify the CRAS point.

First, load up a volume either by passing one on the command line or by using the File menu command or toolbar button. You will see the volume in four views. The top left view is the X projection. The top right view is the Y projection, and the bottom left is the Z. The bottom right view is a 3D view in which you will manipulate a cube to change the rotation.

To change the transform, rotate the cube in the 3D view; you will see the results in the other views. In the 3D view, click and drag with the left mouse button to rotate the blue cube. The blue cube represents the volume orientation. The white outline represents the beginning orientation and will stay constant so you can see what changes have been made. If you click and drag with the middle mouse button, you can rotate the entire view, which is useful if you want to see a different view of the overall rotation. You can click and drag with the right mouse button to zoom in and out. The overall rotation is shown numerically in degrees at the bottom of the 3D view.

As you rotate the blue cube, the results will be shown in the projection views. These through planes are relative to the white outline in the 3D view. You can change the through plane cross section with the slider at the bottom of the view. You can change the brightness and contrast of the view by clicking and dragging with the left mouse button. You can zoom in and out by clicking and dragging the right mouse button, and pan the view with the middle mouse button.

If you need to reset the view, use the View->Restore View command, or click the appropriate toolbar button. This will not affect the rotations you have made, it will just rezoom and recenter the volume in the 3D view.

When you have an orientation you like, you can set the transform in the volume using the Edit->Transform Volume command, or the toolbar button. This will restore the view and you will see the volume in its new orientation. This has not yet saved the transform, though, and you can restore it to the original version in the file with the Edit->Revert Volume command, or the toolbar button.

As an alternate method of changing the transform, you can draw orientation vectors on the 2D views for each axis and create a transfrom from the orthogonalized vectors. To do this, use control-left, middle, and right click and drag to draw the x, y, and z vectors, respectively, on the plane on any 2D view. You can click and drag again to redraw a vector. When you're satisfied, choose Edit->Reorthogonalize Volume. When drawing vectors, think of it as redefining what the cross-section plane will be; for example, when drawing the red vector, you are defining the new x cutting plane (the plane will be orthogonal to the vector). Note that when using this method, you will not be using any rotations currently done by rotating the blue cube unless you have already used the Transform Volume command.

When you are ready to save the transform in the volume, use the File->Save Volume command, or the toolbar button.


Example 1

orient_mri --volume ~/bert.mgz

Open up the volume bert.mgz.





Reporting Bugs

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orient_mri (last edited 2008-04-29 11:45:30 by localhost)