1. User Manual for Tmaptool – T1 ρ processing tool Guruprasad Krishnamoorthy Chetana Bayas Gargi Pednekar

2. System Requirements Processor - Intel Core i5 or equivalent / better Minimum of 4GB RAM MATLAB R2014a 64-bit version or higher C-compiler needs to be installed and associated with MATLAB. Follow the link for more instructionslink

3. Step 1 Unzip the ‘Tmaptool’ folder and make it the current directory or copy the contents to your root directory of MATLAB Run ‘create_MexFile.m’ first. It will compile the C code ‘Tmapfit.c’ to create the MEX file for your OS and MATLAB version If it generates an error, it might be due to the compiler. Either you do not have a compiler or it is not setup yet. Follow the link to setuplink

4. Step 2 Run ‘tmaptool3d.m’. It will prompt you to choose the folder where data is stored. A wait bar with progress will be displayed while reading and it will open a GUI with MPR (Multi-planar reconstruction) of the knee images

5. Step 2_contd Fig 1. MPR_Raw Once the DICOM files are read by the tool, it will open a GUI similar to that of shown in Fig 1. To adjust the window center and width, hold the ‘right-click’ and drag on the axial image. To view different slices of different orientation, click on either Axial, Sagittal or Coronal images. For eg., if you click on axial image. Corresponding Sagittal and Coronal images will be updated. (If you click a voxel of position x-20 y-32, 20 th Coronal slice and 32 nd sagittal slice will be displayed). Once you have visually inspected the data. Click “Start” button. It will prompt you choose one orientation among the three to reformat.

6. Step 3 If you have chosen to reformat the images in Axial orientation, lines will be shown on the sagittal image. If you choose Sagittal or Coronal, lines will be shown on Axial slice The lines corresponds to the Axial slices that are about to be reformatted. Slice thickness can be adjusted by entering the value in the text box. Note that the values should be a multiple of 0.5mm (0.5,1,1.5,2 etc) as the base resolution of the image is 0.5mm 3 Fig 2. MPR_Raw - reformatting

7. Step 3_contd The lines can be rotated to reformat an oblique slice The lines can be moved up or down to set the position The coverage can also be adjusted. The number of slices after reformatting depends on the slice thickness and the coverage. For eg., if slice thickness is set as 3mm and coverage is 18mm, 6 slices are generated in reformatting Once you have adjusted all these parameters as you wish, click on ‘”Reconstruct” button to reformat. This process will take some time and will open an another GUI Fig 2. MPR_Raw - reformatting

8. Step 3_contd Likewise, sagittal and coronal slice can be reformatted by selecting appropriate options by clicking the “Start” button If you choose “coronal” orientation, lines will be generated horizontally on axial slice as shown in Fig 3. If you choose “Sagittal” orientation, lines will be generated vertically on axial slice as shown in Fig 4. Other options viz., coverage, slice thickness etc., will work similar to that of axial reformatting Fig 4. MPR_Raw – Sagittal Reformatting Fig 3. MPR_Raw – Coronal Reformatting

9. Step 4 Once reformatted, the images are loaded to another GUI for Region of analysis (ROI) drawing and processing the data, shown in Fig 5. Fig 5 shows an axial reformatting with slice thickness of 3 mm and coverage of 6mm and hence, 2 slices in total The vertical slider can be used to slide through images corresponding to different TSL of a particular slice The horizontal slider can be used to slide through different slices Fig 5. Display-reconstructed

10. Step 4_contd Click on the button “Draw Mask”. It will create a crosshair when you place the cursor on the image. Draw ROIs on cartilages. In this case, Patellar Cartilage. Once you finish drawing the ROI, right click and choose ‘create mask’. The tool will automatically display the next slice and let you draw the ROI again. Use mouse’s scroll to zoom in and zoom out the image and hold the right click and drag to adjust window center and width In this case, in Fig 6, region marked by green border is the ROI (Patellar Cartilage) Fig 6. Display_reconstructed (Axial)

11. Step 4_contd Reformatted Sagittal and Coronal slices are shown in Fig 7 and Fig 8 respectively To draw ROIs of cartilages on Coronal and sagittal slice, please refer to literatures on the anatomy of knee MRI For coronal slice alone, you will have to draw two ROIs on each slice unlike axial and sagittal. Fig 7. Display_reconstructed (Sagittal) Fig 8. Display_reconstructed (Coronal)

12. Step 4_contd Once the ROI is created. Click on “Divide M/L” button. It will prompt you to draw a line to divide between medial and lateral side as shown in Fig 6 (Zoom in the image to see the detail). Once drawn, double click on the line. Now the tool will prompt you to choose between right and left knee. (choose right knee for this case) You can see a “Segmentation completed!” message in command window once the division is successful Click the Process button to proceed with data fitting. Once the processing is done, it will open another window. Fig 6. Display_reconstructed (Axial)

13. Step 5 Once the data is processed, the tool will open a GUI similar to Fig 7. Use the horizontal slider to navigate through the slider Use edit buttons to adjust Thresholds, window levels and Rsquare thresholds. “Display Rsquare” display rsquare value of the fit spatially as an image. “Save” button will prompt you to choose a folder to save the results. Fig 6. Display_reconstructed (Axial)

14. Step 6 The saved results has two components, 1. Processed images, 2. A text file containing T1 ρ values of cartilages of different compartments of knee. Have Fun!