The three folders contain DICOM stacks that could be output by using functions laid out in iplfe_register3d.txt I could not get this text file to copy over correctly to the Scanco software, but if you run the 'iplfe' command (without quotes) in the Scanco software terminal, you should be able to run the commands on two scans of your choice. This code was built to register two scans of the same bone, imaged at different times.

The MATLAB code will chew through these DICOM stacks and ask for two key pieces of information: the AP axis and medial side. For the AP axis, please choose the anterior side first. Each subsequent scan will default to the same AP axis as the previous.

The scan 1, 2, and difference figures can be navigated by slice #

The TV, BV, BMC, BMD variables are tables that report total volume, bone volume, bone mineral content, and bone mineral density in the anterior, medial, lateral, and posterior quadrants, respectively.

Voxel resolution should be changed in the code if necessary, and the calibration slope and intercept should be machine-specific.

To setup a batch run, change the subjects initialization line to include all of the subjects you want to process. E.g. subjects = ["MARA14-","MARA15-","MARA16-"];

If you would like to repeat the same axes for any two scans, list them together with the first stack being the reference.

PLEASE NOTE: Each time you run this code a new output.xlsx will be written to the code's home directory. This WILL be overwritten if you run the code again.

Update 09/24/24: Now requires a single center dicom nested in a folder called {sub} {location} scan1_raw This is required only from scan1 because scan2 is later registered to scan1. We use this single slice to calculate the medial side and angle of rotation for regional analysis.