Online class

We offer an online class, usually in the beginning of each month, to train you how to use xjview. The cost is $100 (or $50 for students). Please let us know by email (cuixiaofei@gmail.com) if you are interested.

Manual

xjView Videos on Youtube | xjView Videos on Youku

xjView is supposed to be intuitive to use but here are manuals you might find useful:
xjview 8 manual
xjview 4 manual

FAQ

You may check out our google group to see if your question has been answered.

  1. How can I change the colors of each image when I open more than one images?
    You need to change xjview.m source code to change these colors. Colors are controlled by the variable ‘colors’ around line 6589, and the variable ‘colours’ in line 3427.
  2. How can I use Feed function under Mac?
    (from xjview feed)
    line 512: changed ‘callback’,’web(”http://www.alivelearn.net/xjview8/feed.php”,”-browser”)’);
    to ‘callback’,’unix([”firefox “http://www.alivelearn.net/xjview8/feed.php“”])’);
    which you will adapt to your platform (e.g. replace ‘unix’ with ‘winopen’ on Windows) and your web browser…
    line 683: changed web(urls{value}, ‘-browser’);
    to unix([‘firefox “‘ urls{value} ‘”‘]);
  3. Why does the xjview window flicker sometimes?
    If you start SPM before xjview, you might find xjview window flickers – even if you quit spm. To avoid flickering, you should start xjview right after starting matlab.
  4. How can I change the size of xjview window?
    open xjview.m and find the line figurePosition = […]. Change the 3rd and 4th numbers. They control the width and height of xjview window relative to the entire screen.
  5. I have a mask file (mymask.img) and I want to know where the masked region is. What should I do?
    type xjview mymask.img in the command window of MatLab. Then put the cursor in glass view (or section view) to the displayed region.
  6. I have a 23×3 matrix (called A) with each row the MNI coordinate of a voxel. How do I know where the region is?
    type xjview(A) in the command window of MatLab. Then put the cursor in glass view (or section view) to the displayed region.
  7. I have a image file which is the result of a glm contrast. I want to make a mask of the activated region. How can I do it?
    load the image file, change p-value (and cluster size threshold), put the cursor to a region of interest, click “Pick cluster/Info” and save the image by clicking menu File|Save Current Image as Mask….
  8. How many image files can I load at the same time?
    100. But we only have 6 different colors to code them. So it is advisable to load 6 images at the most.
  9. I loaded multiple images, can I change p-Values?
    Yes. xjview will display the supra-threshold voxels for each image.
  10. There is an error when I choose some target images in the section view (such as ch2, ch2bet, aal and brodmann). What happened?
    Those images are not provided by SPM. You may want to check out MRIcro. Copy the corresponding image files (unzipped, with header files) to your spm canonical directory.
  11. Are the coordinates in xjview MNI or TAL coordinates?
    MNI.
  12. My image’s left/right get flipped in xjview (compared to spm). What happened?
    For unknow reasons, in some labs, the coordinate conversion matrix stored in the header of the image file is actually different from that stored in spm.mat which generated the image file. That matrix determines the left/right. To solve this problem, please change the value of variable leftrightflip in the beginning of xjview.m.
  13. What is xBrain?
    (xBrain doesn’t exist any more :)) xBrain is a brain mapping database where you can search a brain region and find out what the function is. Everybody can contribute the database by adding entries.
  14. Where did you obtain the database for anatomical – MNI relationship?
    The database used in xjView is from MNI Space Utility written by Sergey Pakhomov and WFU_PickAtlas by Joseph Maldjian.