Index TableOfContents
Name
orient_mri - graphically and interactively re-orient an MRI volume and save the new transform
Synopsis
orient_mri [--volume VOLUME_NAME [VOLUME_NAME...]]
Arguments
Optional Flagged Arguments
VOLUME_NAME |
Filename of a volume |
The direct file name of a volume, e.g. an .mgz file, a COR-.info file, or a .img file |
Description
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, you will rotate the cube in the 3D view and 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. 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 more isometric view of the overall rotation. You can click and drag with the right mouse button to zoom in and out.
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.
When you are ready to save the transform in the volume, use the File->Save Volume command, or the toolbar button.
Examples
Example 1
orient_mri --volume ~/bert.mgz
Open up the volume bert.mgz.
Bugs
None.
Links
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>