MRIcron: How to look at your brain

  1. Install MRIcron (we provide both Mac & Windows versions)
  2. Open MRIcron, then open the file named ‘ht1spgr.nii’ using MRIcron
  3. If a ‘matrix appears bogus’ message pops up, ignore the message and click OK
  4. 3 pictures of your brain should pop up: a back-to-front view, a right-to-left view and a top-to-bottom view.
  5. Make sure that the Flip L/R option is checked under the View menu
  6. You can navigate your brain by either clicking your mouse or using your keyboard’s arrow keys.
  7. To see your brain from top-to-bottom, scroll across either the top-left or top-right picture
  8. To see your brain from right-to-left, scroll across either the top-left or bottom-left picture
  9. To see your brain from back-to-front, scroll across either the top-right or bottom-left picture
  10. To get rid of the cross hairs when viewing your pictures, click on the button with the blue and red hash mark. Click it again to get them back.
  11. More ways to look at your brain in MRIcron:
  12. Multislice: go to the Window menu and select Multislice. This will show you all of the individual slices!
  13. Render: go to the Window menu and select Render. This will show you what the fMRI thinks you look like!
  14. In the Render window, you can rotate or flip MRIcron’s drawing using the Azimuth and Elevation options
  15. The slide button on the top-right corner of the Render window allows you to see from the outside to the inside of your head!
  16. To adjust the quality of the picture, slide the middle two buttons or click the Shading % button
  17. If you want to play around with the image quality more: go to the Background menu and change either the Air/Skin Threshold or the Search Depth (we recommend Air/Skin Threshold is set to 20 or 30% and Search Depth is at 2 or 4 voxels)
  18. IMPORTANT: If you click on the rendered picture and it disappears, don’t panic; close the Render window and go back to the Window menu and hit Render again.
  19. To save the picture on your screen go to the File menu then select Save as Bitmap.
  20. IMPORTANT: This saves a picture of whatever is on the MRIcron screen, so if you have cross hairs selected, the picture will also have these cross hairs.