These instructions work with this dataset from Franco Pestilli. Try the directory STN/sub-FP.

1. Set mlrPath First make sure that you have mrTools in your path and then run mlrPath to make sure it does not conflict with vistasoft

   mlrPath mrTools+vista

   This will make it so only mrTools is in your path as well as a few vistasoft paths that do not conflict. You will also need to have mba in your path.

2. Install Plugin You need to first setup the mlrLife and mlrAnatomy plugins by doing

   mlrPlugin('altPlugins');

   and selecting mlrLife and mlrAnatomy. This should be done before starting mrLoadRet.

3. Create empty MLR session Make an empty MLR session for loading the anatomies

   makeEmptyMLRDir('mlr')

4. Start MLR Start MLR by switching to the directory you just created and run mrLoadRet
5. Import fascicles Import fascicles by going to File/Base Anatomy/Import Fascicles
6. Choose dwi Choose the original DWI nifti file from which the tracts were created. This file is opened just to get the header information.
7. Choose tck Next choose the tractography file you want to load
8. Choose subset number For now the code is slow, so choose the number of random fibers that you are going to load - a number like 5000 works ok.
9. Fix T1 header All the headers have sform and qform codes set to 2 - which is not recognized by MLR - so fix the T1 header to have qform and sform code set to 1.

   cd Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes/STN/sub-FP/anatomy
   [d h] = mlrImageLoad('t1.nii.gz');
   h.hdr.qform_code = 1;
   h.hdr.sform_code = 1;
   mlrImageSave('t1_sform_code_fix.nii',d,h);

10. Load T1 Now go to File/Base Anatomy/Load and load the t1_sform_code_fix nifti file you just created.Select the 3D radio button and rotate the anatomy so that you can see it.
11. Set multidisplay Go to View/Multi Base Display and select it. Then in the panel to the right, select the tract base and click MultiDisplay. You may also want to change the Overlay to a color that is easily viewable. Should look like the following: