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| If you left click and drag on a plane, you will a red crosshair on the plane, and the voxel value at that cross will be displayed. Middle clicking will actually move the plane. If you middle click on the inside portion of a plan, you can translate the plane along the axis, and if you click near the outside, you can roate the plane. This may take some time to get used to. | If you left click and drag on a plane, you will see a red crosshair on the plane, and the voxel value at that cross will be displayed. Middle clicking will actually move the plane. If you middle click on the inside portion of a plane, you can translate the plane along the axis, and if you click near the outside, you can roate the plane. This may take some time to get used to. |
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 CRAS transform). You can rotate the volume to a new orientation, check the cross section, and save the transform.
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 the main view in the same orientation in which tkmedit or scuba first displays it. You will see three cross-section planes displaying slices, a white outline that shows the outline of the volume, and the exes in green, red, and yellow.
Clicking and dragging outside of the planes will orient the volume. Click and drag with the left mouse button to rotate the volume. Middle clicking will pan the view, and right clicking will zoom. Note that only rotating that volume will have any effect on the final transform; the other functions are just for moving the camera. You can also zoom in and out with the commands in the View menu, or with the appropriate toolbar buttons.
If you left click and drag on a plane, you will see a red crosshair on the plane, and the voxel value at that cross will be displayed. Middle clicking will actually move the plane. If you middle click on the inside portion of a plane, you can translate the plane along the axis, and if you click near the outside, you can roate the plane. This may take some time to get used to.
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 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>