Bone Mask Generation from 3D Slicer Generated File and Statistical Analysis of Identified Bone Erosion in Rheumatoid Arthritis Patients

To begin, launch the 3D Slicer software. For image input of the identified bone erosion sites, click on the button labeled Data on the 3D Slicer window. Then press Choose Files to add and locate individual images to add the files.

To import an entire directory of images at once, press the Choose Directory to Add option, then search and insert the preferred directory. Next, click on the dropdown menu of the 3D Slicer's toolbar. Hover the cursor over the bone analysis modules and click on Automatic Mask.

Under the tab Step 2 Automatic Mask, choose an input volume from the input volume dropdown menu. Select Create New Label Map Volume in the output segmentation dropdown menu. If another output label is preferred, click on Create New Label Map Volume As and provide the desired label.

Input the number of bones to be masked in the given text box, then select ORMR or Dual Threshold from the algorithm dropdown menu. Click on Get Mask to run the algorithm and output a result in the corresponding image directory. If the image contains multiple bones, a separate mask will be saved for each one.

To import a binary mask onto 3D Slicer, copy the mask files onto the load masks directory located in the BAM folder. Go back to the 3D Slicer window and click on the tab Step 3 Manual Correction. To load the mask files and automatically convert them to slicer segmentations, click on Load.

To make changes to the mask, use the tools provided in the manual correction tab. To start statistical analysis, click on the erosion volume module from the dropdown menu on the toolbar. Load an image and its corresponding mask.

Select the input image and mask, create an output segmentation, and place the seed points on the erosion. Click on the Get Erosions button to initiate the erosion measurement algorithm. If the size and shape of automatically detected erosion volumes are unsatisfactory, manually edit them under the tab Step 5 Manual Correction.

Now click on the tab labeled Step 6 Statistics to export the computer data into a spreadsheet file. Next, input the erosion volume in the dropdown menu labeled Input Erosions. Now provide the gray scale image and its voxel width in millimeters in the text box under the master volume menu.

Click on Get Statistics to generate a spreadsheet file in the Erosions Output Data Directory located in the BAM folder.