Comparing cortical data in low and high resolution scans

The first step is to load the two surfaces we wish to compare (File->Load surfaces, select the two .ply|.wrl files by clicking on the first and ctrl-clicking on the second). wxRegSurf decides which is the low resolution (LR, red) surface and which is the high resolution (HR, green) surface by counting vertices. It is important that the LR filename includes the string femur, since there are some minor differences in the way wxRegSurf's algorithms are tuned for different bone types. We now wish to align these surfaces using a seven degree-of-freedom similarity transformation (Registration->Similarity). The alternative is to use a rigid registration, though the extra scale parameter allows for scanner calibration errors and systematic segmentation differences. wxRegSurf calculates a rough, initial alignment by analysing the surfaces' shapes and topologies. If this fails, directly manipulate the LR surface (Mouse->LR surface, left/middle mouse button to rotate, right mouse button to translate, scrollwheel to scale, single click to reflect) until the surfaces are roughly aligned.
By default, wxRegSurf matches each vertex on the LR surface with the closest vertex on the HR surface, as long as the distance between the vertices is less than the Search range. To see these matches, click Show matches. wxRegSurf's registration algorithms aim to minimize the summed lengths of these matches. In this example, we see a common complication with the LR surface extending below the HR surface. If we registered with these matches, the LR surface would rise too far up the HR surface, in a misguided attempt to minimize the lengths of the matches at the bottom.
We could try to remove these unwanted matches by restricting the Search range (and sometimes such adjustments are useful), but the easiest way to proceed is to set Match rims to No. This removes all matches between LR vertices and vertices on the open rim of the HR surface. We now have an appropriate set of matches and are ready to register.
Next, we set the Iterations slider to something suitably high and press Start. At each iteration, wxRegSurf finds the transformation that minimizes the summed lengths of the matches and then recomputes the matches. After a short while this process converges to a stable alignment and we can either interrupt it (Stop) or wait until the iteration count is reached. File->Save registration saves the alignment in a .reg file.
The next stage of the analysis is to load the cortical data for the LR surface (File->Load surface data, choose between the sw thickness file, sw density file and surface data file filters, then select the appropriate .bin file). wxRegSurf will quietly load any corresponding error file it finds in the same directory: these contain precision estimates at each vertex and are used to weight any data smoothing we might perform. The filenames for the cortical data must terminate in either _thickness.bin (Stradwin thickness), _density.bin (Stradwin density) or _dat.bin (general surface data).

To see the data we have loaded, we select Surface shading->Surface data. In this example, we see a rather poor estimate of cortical thickness obtained by simple thresholding. The white areas are where the CT data did not exceed the threshold.

Next, we load the cortical data for the HR surface (File->Load surface data again). To visualize this data clearly, without the obscuring clutter of the LR data, we uncheck the Show LR checkbox. It is clear that this data was measured at a much higher resolution: the CT scans were performed in a high resolution pQCT system, as opposed to conventional clinical CT for the low resolution scans.
wxRegSurf compares each LR data value with its matched HR value (Show matches). For such a comparison to be meaningful, it is first necessary to smooth the HR data until it matches the spatial resolution of the LR data. Every time we press the Smooth button, wxRegSurf replaces each data value with a weighted average of immediately neighbouring values, with the weights set according to the precision estimates found in the error file. If there is no error file, uniform weighting is used. wxRegSurf smoothes any data that is currently displayed, so if we only wish to smooth the HR data, we must ensure that the Show LR checkbox is unchecked.

How much smoothing is necessary? This depends on the resolutions of the scans and the average edge length in the HR mesh. We need to calculate (elsewhere, wxRegSurf cannot help with this) how many smoothing cycles are required to blur the high resolution point spread function such that it approximates the low resolution point spread function.

Finally, we can visualize the Signed data error or the Absolute data error: the latter is shown on the left. These errors are displayed on the LR surface, so we check Show LR and uncheck Show HR. The results can be saved by selecting File->Save LR-HR map. This writes a comma separated variable (.csv) file with four columns. The first is the index of each LR vertex, the second is the index of the matched HR vertex (or "unmatched"), the third is the LR data which may be "invalid", and the fourth is the (smoothed) HR data which may be "unmatched" or "invalid". The .csv file is named automatically, according to the two cortical data files that were loaded and compared. It may be read into a spreadsheet or other software for further analysis.

We might wish to repeat this process for tens or hundreds of bones. wxRegSurf provides a mechanism for sequential processing using batch (.run) files. An example batch file is shown below. We could cut-and-paste these lines into a file called, for example, MyBatchFile.run. A batch file can be run from the user interface (File->Load and run batch file) or by supplying its name as a command line argument when wxRegSurf is invoked.

/path/to/surface/and/data/files/including/trailing/slash/

# LR surface  HR surface    LR data                 HR data                 reflect  smth LR  smth HR  range  fussy    n iter  reg type  save reg  save LR data  save map  review       rims
#                                                                                                             -1=auto          -=as->sm            -1 = no                 0 = no       0 = no
#                                                                                                                                                  0 = yes                 1-6 = angle  1 = yes
#                                                                                                                                                  >0 = smth               - = LR only  2 = to rims

# register
lr_femur.wrl  hr_femur.wrl  n/a                     n/a                     0        0        0        999    0        200     1         1         -1            0         0            0

# review
lr_femur.wrl  hr_femur.wrl  n/a                     n/a                     0        0        0        999    0        200     1         0         -1            0         1            0

# map
lr_femur.wrl  hr_femur.wrl  lr_femur_thickness.bin  hr_femur_thickness.bin  0        0        20       999    0        0       1         0         -1            1         0            0

A batch file may include any number of blank or comment lines. The first non-comment line contains the full path to the working directory, where wxRegSurf will look for .ply|.wrl and .bin files. Each subsequent line contains a set of instructions for wxRegSurf to load files, process them and then save the results. Draft batch files can be produced using wxRegSurf's automatic batch file writer, then edited manually as required.

In the example above, the first line loads two surface files (but no thickness or density files) and registers them with a similarity transformation (reg type is 0 for rigid, 1 for similarity, 2 for similarity+FFD and so on, mirroring the options in the Registration choice control). The search range is effectively unconstrained (999) but rim matches are excluded (this is indicated by the 0 in the penultimate column). 200 registration iterations are performed before the results are saved in a .reg file. We could fill the batch file with hundreds of similar lines, registering different pairs of bones, and leave wxRegSurf to run unattended.

Following registration, we must check that all bones were aligned satisfactorily. This is what the second line does in the example above. It performs 200 iterations in "review" mode, whereby the surfaces are loaded and spun around for the user to inspect. Lower numbers of iterations reduce the inspection time, higher numbers increase it. Alternatively, we could set the iteration count to zero, in which case wxRegSurf instead saves a snapshot of the aligned bones (.png) for offline inspection. Changing the review flag from 1 to some other number saves a different view (1=front, 2=left, 3=back, 4=right, 5=top, 6=bottom). Any misregistered surfaces must be corrected manually, with the updated results saved to the .reg file.

The final line of the above example loads the two sets of cortical data, performs 20 smoothing cycles on the HR data, applies the similarity transformation from the .reg file, matches the LR and HR vertices over an effectively unconstrained search range but excluding rims, and then saves the LR-HR map in a .csv file.