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Scuba, unlike tkmedit, displays all data in a global coordinate space called RAS space (for Right-Anterior-Superior). The unit of this space is centimeters; (0,0,1) is 1cm 'above' (superior) to the origin.
Tkmedit and other FreeSurfer tools, on the other hand, usually view all data in reference to a single volume. When other volumes want to be viewed overlayed onto the main volume, they are 'registered onto' that volume. Scuba has no main volume; all volumes are transformed into RAS space by built-in transforms set by the scanner, commonly called the MRI-to-RAS transform, or index-to-voxel transform. However, don't let the term 'voxel' confuse you, as it can also have MRI or index voxels and RAS voxels.
When 'registering' a volume 'onto' another one in scuba, the user must specify source and destination data collections. This is because some FreeSurfer registration transforms use inherent geometry information to register volume, which is normally transparent to the user due to the assumption of a 'main' and 'movable' volume.
Ultimately, it may be necessary to play around with the configuration settings in scuba to mimic tkmedit or tkregister style registration behavior. It's not so bad though.
Loading the Data
A common use of registration transforms is to view a high resolution volume overlayed onto a low resolution volume in which the hires volume is a 'blown up' region of the lores volume. In this case, the lores volume is the fixed volume and the hires volume is the movable one, in tkregister terms. The transformation matrix registers the movable volume to the fixed one.
First, load up the volumes and the transform. This can be done via the command line:
scuba -v lores.mgh -v hires.mgh -t transform.xfm
The order is not essential, but in the order, the lores volume will be put in draw level 0 and the hires will be put in draw level 1, putting the hires volume 'on top' of the lores volume, which is what we want.
Configuring the View
The first thing you may way to do is configure the layers so you can see the overlay properly. If your movable volume is smaller than your fixed target, i.e. in the hires/lores case, you will probably want to use the min/max visible value slider on the hires layer to 'cut out' the area around the volume so you only see the hires area of interest. Or you may want to reduce the opacity so the hires layer is slightly transparent. These tasks can be done in the Layers panel. Be sure your hires volume is selected in the pull-down menu at the top of the Layer panel.
Setting up the Transform
Now tell the movable volume to use the transform we loaded. In the Data Collections panel, make sure the movable volume is selected in the pull-down menu. In the Transform menu below the entry field, select the transform we just loaded. You should see the movable volume 'jump' as it is now displayed with this transform. (If you do not see an immediate update, you may need to 'wiggle' the view; move the mouse inside the view and press the arrow keys a few times.)
If this doesn't look right, you need to tell scuba that this transform is a 'registration' transform as output by tkregister or other FreeSurfer tools, and to use the geometry information in the fixed and movable volume. In the Transforms panel, select the transform in the pull-down menu. Click the "Treat as Registration" button below the entry fields and select the fixed and movable volumes from the menus. You should see the movable volume displayed in a new location. If it still doesn't look right, try switching the fixed and movable volumes as specified in the pull-down menus.
It Still Doesn't Look Right
If this still doesn't look right, your transform may not be compatible with scuba, or the transformation process may be specific to tkregister. If this is the case, email KevinTeich for help.