xjView 4.0

a viewing program for SPM2 and SPM5

... a VERY useful viewing program that is small and easy to use. p-value slider, id of anatomy with a single mouse click, etc.

 from Imaging and Unix Glossary @ CNL @ University of Arizona

Interface

Geographic distribution of xjView users (as of 10/8/2008), 4890 downloads

about this program

xjView is mainly a viewing program for SPM2 and SPM5. With xjView version 4 you can:

  • Easily change p-Value by sliding a scroll bar and display the resulted supra-threshold voxels instantly.
  • Display multiple images at the same time and find the common regions. (Common regions are displayed in intermediate colors.)
  • Pick up one or more clusters and save them as a mask image for future ROI analysis.
  • Find out the anatomical name of the selected voxel or cluster(s).
  • Search the selected brain regions in databases (xBrain, google scholar and pubmed) and find out what the function is.
  • Display the images in glass view, section view and 3-D render view.
  • Display a T-test image with positive T coded by hot color and negative T coded by cold color.
  • Overlay a known structure (e.g. Brodamnn 10) to the current hot spot.
  • Data preprocess, GLM estimation, ROI analysis, etc
  • And more ...

    • xjView was written by Xu Cui (blog) and Jian Li at Human Neuroimaging Lab at Baylor College of Medicine. The database used in xjView is from MNI Space Utility written by Sergey Pakhomov and WFU_PickAtlas by Joseph Maldjian.

    Xu Cui is now a postdoc at Stanford University and Jian Li is a postdoc in New York University.

    For bugs or comments, please send a message to cuixiaofei AT gmail dot com

    update

  • 2007-11-21: aal antatomy added.
  • 2007-2-13: xjView now works under spm5 (both updated and original release).
  • 2006-12-06: It seems xjview doesn't work under updated spm5 (though it works under the original version of spm5). It will give an error about 'snap' and the glass view is also wrong. We are updating xjview.
  • 2006-06-26: xjview 4 manual available in pdf
  • 2006-06-16: xjview now works under both SPM2 and SPM5 (original version).
  • 2006-06-07: left/right flip issue solved. Users are required to change a variable called leftrightflip in the beginning of file xjview.m.
  • 2005-12-29: xjView 4 released
  • Previous versions

    • download and system requirement

    To run xjView you need:

    • MatLab 6.5 or above
    • SPM2 or SPM5 (add SPM to your MatLab path)

    Simply fill out your information and click "Go to download page" button. The information is used for statistical purpose only.

    Your name
    Your institute
    Your email

    usage

    There are 4 ways you can start xjView in MatLab command window (type help xjview):

    After you start xjView (and open an image file), the main screen will look like this (click to view larger figure):

    1. Menu bar. This menu bar is a standard MatLab figure menu bar, with some changes in blue.
    2. Glass view.
    3. Section view.
    4. Render view. (You have to check "Render view" to display. Note: displaying render view takes considerably longer time than glass view and section view and thus you might want to check the render view only when necessary.)
    5. Information window. Warnings, errors or status will be shown here.
    6. Control panel.
    7. Anatomical description (in Talairach Atlas Labels) of the pointed voxel.

    File Menu

    1. Open an image file or multiple image files. For example, a T-test image files. You can also double click mouse in any blank space to open image files.
    2. Save the currently displayed image to an image file. The intensity values are also saved.
    3. Save the currently displayed image to an image file, with all displayed voxels having intensity 1 and others 0.
    4. Save the whole figure in ps/pdf format. (not recommended. I myself use 'print screen' and paste to Microsoft Paint to output the result.)

    Control Panel

    1. Search a brain region (in edit box 9) in an online database (10, xbrain, google scholar, or pubmed).
    2. Overlay a known brain structure (in the right edit box). You can choose the known structure from the list (11).
    3. List supra-threshold voxels.
    4. Select positive, negative or all values to display.
    5. Cluster size threshold.
    6. pValue/T/F threshold.
    7 Slider, to change pValue continuously.
    8. Current voxel.
    12. If multiple images are opened, click 'common region' to display the common region only.
    13. Display render view.
    14. Select and Pick cluster. If a cluster is picked, the cluster information will be displayed in information box. For example,
       # voxels structure

       10 --TOTAL # VOXELS--
       10 Left Cerebrum
       10 White Matter (L)
       6 Frontal Lobe (L)
       5 Sub-Gyral (L)
       4 Extra-Nuclear (L)
       4 Sub-lobar (L)
       1 Inferior Frontal Gyrus (L)

    Help Menu

    1. Go to xBrain.org website. (click figure below to view larger figure)

    xBrain.org is a growing database where you can find the functions of a certain brain region. With full access, you can see the pictures of that region and the full-text source paper, etc.
    2. xjView help (simply go to this page you are reading).

    xjView in publication

    Cui X, Jeter CB, Yang D, Montague PR, Eagleman DM. (2007) Vividness of mental imagery: Individual variability can be measured objectively. Vision Res. 47(4):474-8

    Li J, McClure SM, King-Casas B, Montague PR. (2006) Policy adjustment in a dynamic economic game. PLoS ONE. 1:e103

    Stetson C, Cui X, Montague PR, Eagleman DM. (2006) Motor-sensory recalibration leads to an illusory reversal of action and sensation. Neuron 51(5): 651

    Summerfield C, Greene M, Wager T, Egner T, Hirsch J, et al. (2006) Neocortical Connectivity during Episodic Memory Formation. PLoS Biol 4(5): e128

    Q & A

    Q 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.
    Q I have a 23x3 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.
    Q 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....
     Q 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.
     Q I loaded multiple images, can I change p-Values?
    Yes. xjview will display the supra-threshold voxels for each image.
     Q Can I load a T test image, an F test image, a mask image, and another image file from an unknown source at the same time?
    Yes. But don't confuse yourself before confusing xjview.
     Q 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.
     Q Are the coordinates in xjview MNI or TAL coordinates?
    MNI.
     Q 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.
     Q What is xBrain?
    xBrain (http://www.xBrain.org) 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.

    Last update: 8 Oct 2008

    This webpage is maintained by Xu Cui (cuixiaofei AT gmail dot com)