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
a. If a ‘matrix appears bogus’ message pops up, ignore the message and
click OK
3. 3 pictures of your brain should pop up: a back-to-front view, a right-to-left
view and a top-to-bottom view.
a. Make sure that the Flip L/R option is checked under the View menu
4. You can navigate your brain by either clicking your mouse or using your
keyboard’s arrow keys.
a. To see your brain from top-to-bottom, scroll across either the top-left
or top-right picture
b. To see your brain from right-to-left, scroll across either the top-left or
bottom-left picture
c. To see your brain from back-to-front, scroll across either the top-right
or bottom-left picture
5. 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.
6. More ways to look at your brain in MRIcron:
a. Multislice: go to the Window menu and select Multislice. This will
show you all of the individual slices!
b. Render: go to the Window menu and select Render. This will show
you what the fMRI thinks you look like!
i. In the Render window, you can rotate or flip MRIcron’s
drawing using the Azimuth and Elevation options
ii. 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!
iii. To adjust the quality of the picture, slide the middle two
buttons or click the Shading % button
1. 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)
iv. 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.
7. To save the picture on your screen go to the File menu then select Save as
Bitmap.
a. 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.