Perelman School of Medicine at the University of Pennsylvania

Center for Magnetic Resonance & Optical Imaging

T1rho and T2 processing

This MatLab GUI will assist in the generation of T1rho or T2 parametric maps from DICOM-type MRI data.  

To run:

  • Extract *.rar file into */Documents/Matlab
  1. Open MatLab and –> File –> Set Path –> Add with Subfolder
  2. Select top level folder of extraction
  3. In the command line, type “generate_tmap”
  4. A window will pop up asking “How Many Sets?”  This is asking how many time points will you be using (different TEs or Spine-Lock times).  Can take up to 10 points
  5. In new window, select “Set 1” through your last set.  Each time, select the directory with each time point of data.  Each directory can only have DICOM files in it and should be sorted by slice number.  
  6. When all stacks are loaded, you can change image to view (Radio Buttons) or slice number (slider bar)
  7. Make sure that times are correct for each stack (times in ms)
  8. Coregistration is optional and works better if image has been cropped to only incorporate rigid-body motions.  Examples where cropping is necessary include knees where the bone may rotate between images but the muscle & fat tissue does not move.   Coregistration will only correct in-plane rotations and translations.
  9. To crop, “Select Crop Region” and click once for top left hand corner of crop box and click once for bottom right hand corner of crop box.  A window will pop up showing the crop region.
  10. To crop entire data set, click “Crop all Images”.  Cropping can be redone by clicking “reload all images”.
  11. If multiple slices are used, it may not be necessary to keep all slices in the stack for map generation (region of interest may only be in middle slices).  You can focus on the relevant slices by clicking “Select Slices to be Used” and specify first and last slice.  
  12. Select “Coregister images” if necessary.  Image will disappear and a radio button will need to be selected again.  
  13. Create map by selecting “Generate Map”.  Images can be eliminated from map generation by unselecting the checkbox for each image.  
  14. Click save images to save data.  The output includes the co-registered/cropped images in DICOM format and the raw data & parameteric maps in original *.mat file.  It does not matter if you select generic, axial, or coronal – that specifies different labels in the *.mat file.
  15. Select restart to re-run the program.

For any questions email :