In addition to manually aligning data sets (described at the section called “Manually Aligning Data Sets”), data sets can also be aligned using the alignment wizard utilizing either mutual information or fiducial markers.
A rigid body alignment can be performed utilizing mutual information between two data sets. This algorithm works by taking orthogonal slices from one data set (transverse, coronal, and sagittal) and computing a transform to best allow matching of these slices to the second data set. This algorithm works best when the two data sets have already been roughly aligned. Note that the orthogonal slices utilized for the matching are derived utilizing the current viewing parameters (current viewing location, slice width, interpolation method, etc).
A rigid body alignment can be performed utilizing fiducial markers. The process is basically:
Draw at least three pairs of fiducial makers between the two data sets that you wish to align. Drawing fiducial markers is described below as the section called “Drawing Fiducial Markers”.
Run the alignment wizard (under tools->alignment wizard). For the alignment wizard to recognize two fiducial markers as a pair, they must have exactly the same name. So if you have a marker labeled "1" under the first data set, you will need another marker, also labeled "1", under the second data set.
Fiducial markers can be added to any of the data sets in the study in a variety of ways. For the currently active data set, hitting the "Edit->Add fiducial mark" menu item will drop a fiducial maker at the currently viewed location. Fiducial marks can be added for the active data set directly from the views by pressing ctrl-right mouse button, which will drop a fiducial marker at the point that the mouse is currently at. Finally, fiducial markers can be added to non-active data sets by pressing ctrl-right mouse button while hovering over a data set's name in the study list.
After being created, the fiducial marker can be moved by clicking on the marker point shown in any of the views.
Coming soon. Note that only what is strictly inside the cursor lines is saved. What's underneath and outside the cursor lines is cropped away.
The factor analysis wizard is currently being developed. It probably won't work for you, and is only included in AMIDE for those who might be interested in working on it (rather than with it).
Nothing written yet...
Note, will generally get much better results for fly through if using trilinear interpolation.
A complete description of this tool has not yet been written.
The left and right limits of the gaussian fit can be altered by clicking on the profile with the left and right mouse buttons, respectively. The x value used for initializing the gaussian fit can be picked by clicking on the profile with the middle mouse button.
Note that the line profile is extracted from the currently viewed image, not the underlying raw data itself. This means things like the current interpolation and FOV will effect the line profile that's generated, and as such may effect the FWHM that's fitted.
A description of the ROI statistics tool can be found at: the section called “Calculating Statistics”.