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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. 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.
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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. 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.
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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. 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.
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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. 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.
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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. 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.
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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 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.
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When you are ready to save the transform in the volume, use the '''File->Save 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. 

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

FreeSurfer

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

KevinTeich

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