AD: MP3 Conversion of Raw Data

Once you have downloaded and unzipped your raw data and moved it into a folder named ‘Raw Data’ on the network drive, follow the steps outlined below to convert your data, using the ‘Medical Software for Processing Multi-Parametric Image Pipeline (i.e. MP3).

1. Create a folder named ‘Converted data’ in your network drive and create subfolders for each subject. This is where you will move the converted data into, after you perform MP3 conversion.

2. Create a temporary folder in your network drive and name it ‘TEMP’. This is where all of your converted data will end up as you convert each subject.

3. Open a new MATLAB window.

4. Type '1' in the command window.

5. Drag and drop the MP3 startup file into the MATLAB command window (startup file is the ‘MP3’ MATLAB code file located in Z:\Sys Admin\MP3). The following window will open:

Open

6. In the above window, click ‘File’ → ‘New project’ and then select the file path of the ‘TEMP’ folder you created in step 2. This will create an ‘MP3_database’ file and 2 sub-folders: ‘Raw_data’ and ‘Tmp’, in the ‘TEMP’ folder.

7. In the MP3 window, click ‘File’ → ‘Import data’ → ‘Import raw data’ and the following window will open:

Open

8. Click the ‘Bruker' icon, which is highlighted in the above screenshot, and select the folder path of your ‘Raw Data’ folder which contains the downloaded raw data.

9. In the middle panel, select a subject who’s data you wish to convert e.g. subject 'M172'.

10. Hold the ‘shift’ key and select all of the images in the left hand pane, then hold the ‘Ctrl’ key and click on the plot to unselect it (otherwise the conversion will not work), in this example, number '15', circled in red below:

11. Right click the highlighted images in the bottom panel and click ‘Add to basket’.

12. In the top left hand corner next to the ‘Home’ tab, click the ‘Basket’ tab, and click ‘export to MP3’.

13. Once the conversion is complete, click ‘Ok’ on the message box that pops up and then click ‘Ok’ in the following 3 message boxes that pop up. This will move the converted files from the ‘Tmp’ folder to the ‘Raw_data’ folder, in the ‘TEMP’ folder you created.

14. Move the converted files from the ‘Raw_data’ folder into the corresponding subject’s folder in the ‘Converted data’ folder you created in step 1.

15. Create a new ‘Tmp’ folder in the ‘TEMP’ folder, as it is deleted once the files are moved to the ‘Raw_data’ folder, in step 12.

16. Click back on the ‘MRI Files Manager’ window you had open in step 10 and click on the ‘Home’ tab in the top left hand corner.

17. Click on another subject in the middle panel and repeat the process to convert the next subject’s data.

18. Once you have converted the raw data for all subjects, delete the ‘TEMP’ folder, close the ‘MP3’ MATLAB windows, and follow the instructions on the next confluence page ‘Sorting Files into Subject Folders’.