Home > brain, matlab > xjView, a viewing program for SPM2, SPM5, SPM8 and SPM12

xjView, a viewing program for SPM2, SPM5, SPM8 and SPM12

October 24th, 2008

xjView’s official webpage moves to http://www.alivelearn.net/xjview/

xjView Interface

xjView Interface

xjView is a MatLab program Jian and I wrote a few years ago to display SPM T-test images more easily. Main features include

  1. p-value slider: change p-value and display the supra-threshold activation instantly
  2. anatomical description: tell you if this is hippocampus or thalamus
  3. display more than one images together: so you can compare activations from different contrast
  4. single out an activation region and get statistics of “how many voxels are in what region”

xjView also has a powerful functional-image analysis package. Some calls SPM analysis functions (e.g. GLM) in a batch mode, some were written by myself (e.g. ROI plotting). You probably need some time to learn how to analyze using xjView; but once you learn it, it allows you to analyze your entire data (say 20 subjects) in one day!

link: xjView official website

Author: Xu Cui Categories: brain, matlab Tags:
Try Stork, a research tool we developed

Stork is a publication alert app developed by us at Stanford. As a researcher we often forget to follow up important publications - and it's practically impossible to search many keywords or researchers' names everyday. Stork can help us to search everyday and notifies us when there are new publications/grants. How Stork helped me?

About the author:

Xu Cui is a human brain research scientist in Stanford University. He lives in the Bay Area in the United States. He is also the founder of Stork (smart publication alert app), PaperBox and BizGenius.

 

He was born in He'nan province, China. He received education in Beijing University(BS), University of Tennessee (Knoxville) (MS), Baylor College of Medicine (PhD) and Stanford University (PostDoc). Read more ...
  1. April 23rd, 2009 at 03:16 | #1

    xjView is being updated right now. The new version will be called xjView 8 and will have the following updates:
    1. compatible with SPM8
    2. add slice view (or montage view)
    3. have an option to render the brain in “old” style
    4. single click to have a summary of the current image (including # of clusters, peak MNI coordinate of each cluster, anatomical description of each cluster etc)

  2. May 28th, 2009 at 10:08 | #2
  3. June 8th, 2009 at 03:44 | #3

    You can download here
    http://www.alivelearn.net/xjview

  4. lchy1978
    June 18th, 2009 at 15:09 | #4

    dear Pro.Cui:
    hello,I have a question about Xjview ,this is:
    # 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)
    how to understand the number?the total of voxels in left cerebrum donot accord with White Matter (L) ,Frontal Lobe (L) , Sub-Gyral (L) , Extra-Nuclear (L), Sub-lobar (L), Inferior Frontal Gyrus (L),why?
    look forward to receiving your help,thank a lots
    lchy1978

  5. June 18th, 2009 at 15:38 | #5

    The number means “how many voxels are in xxx region”. The regions listed are not exclusive, meaning a voxel can be both in (e.g.) White Matter and Frontal Lobe. In your case, you have 10 voxels in total; 10 of them are in Left Cerebrum, 10 of them are in White Matter, etc.

  6. burak
    July 9th, 2009 at 06:12 | #6

    @Xu Cui

    Dear Xu,
    Thank you for these amazing program,
    But the link for the manual is not working..
    Do you know a way to get the manual.
    many thanks
    burak

  7. July 9th, 2009 at 10:00 | #7

    @burak
    I will try to put the manual there.

  8. July 11th, 2009 at 05:01 | #8
  9. Shelli
    October 18th, 2009 at 13:39 | #9

    Xu, is there a way to choose what slices are shown in the slice view? For example, I want to display only transverse slices -16 to 44?

  10. October 18th, 2009 at 14:06 | #10

    @Shelli
    Shelli, xjview doesn’t offer an explicit option to do that. But it should be fairly easy to do a screen capture and cut extra slices in an image editor (such as photoshop).

  11. sarika
    March 4th, 2010 at 22:15 | #11

    Hi,
    Our lab recently started using xjview and it has really made our lives easy!I have been having some trouble interpreting the deactivations in xjview and i would be grateful if you can suggest a solution to these:
    (1)SPM uses contrast maps (con.img), hence would it be better to use contrast maps itself in xjview? Will using t-maps (spmT.img) make a difference in results?
    (2)The deactivation volumes obtained through xjview are not obtained through SPM.Is there a way in which I can calculate the beta values for individual subjects using the deactivation volumes obtained in xjview?
    (3) Can the negative z-scores shown in xjview be directly interpreted as deactivations?

  12. March 5th, 2010 at 03:17 | #12

    @sarika
    (1) SPM displays T-test image (not contrast image) in result. They are different. Contrast image saves the difference of beta values, but T image saves the significance (or T value) of the difference.
    (2) Assume you have 2 conditions, flash and beep, in your experiment. There will be some regions (e.g. visual cortex) which show greater activity for flash than beep; at the same time, there will be some regions (e.g. auditory cortex) which show greater activity for beep than flash. A contrast of flash-beep will reveal both auditory cortex (positive) and visual cortex (negative). Negative value in visual cortex doesn’t mean “deactivation” of this region, it simply means this region shows less activity in beep than in flash. While SPM only displays one direction (positive direction), spmT images store both information. xjView can show both direction at the same time.

    You can’t calculate beta for individual subjects using negative volumes.

    (3) No. See point 2 above. btw, it’s usually T-score.

  13. Ben
    March 31st, 2010 at 06:58 | #13

    Hi,

    I have a basic question. How can I change the color of maps intensity representation with multiple image files? The reason is I want to use montage view, but default is to make the second image colormap yellow, which does not show up very well in publication. When I try to go in and change color properties in Edit->colormap nothing happens.

    Best,
    Ben

  14. March 31st, 2010 at 07:05 | #14

    @Ben
    inside xjview.m, find function spm_sections, around line 6570, you will find line:
    colors = repmat([1 0 0;1 1 0;0 1 0;0 1 1;0 0 1;1 0 1],20,1);

    You can change colors of overlay. Each row defines a color in R-G-B value.
    e.g. 1 0 0 means red.

    To change the corresponding legend color, find function
    CallBack_loadImagePush, around line 3411
    colours = repmat([1 0 0;1 1 0;0 1 0;0 1 1;0 0 1;1 0 1],100,1);

    you should change to same colors.

    Hope this helps.

    Xu

  15. Jordan Poppenk
    April 14th, 2010 at 04:20 | #15

    Thank you for continuing to develop this superb utility. I find it very useful for visualizing and documenting output from many of the standard and experimental analyses that I run (most of which do not involve SPM).

  16. clarissa yasuda
    July 25th, 2011 at 12:18 | #16

    Dear Prof. Xu

    I would like to know how to change the first color to blue/green, instead of yellow/red..

    I changed the colours when I select 2 t-maps, but I also would like to make pictures with deactivations in blue, instead of red/yellow.

    Thanks in advance
    clarissa

  17. July 26th, 2011 at 10:45 | #17

    @clarissa yasuda
    Is my answer to Ben above helpful? Here

  18. clarissa yasuda
    July 30th, 2011 at 13:24 | #18

    Dear prof. Cui

    I tried these suggestions and I could change the colors of multiple maps. But not for a single T-map. Even with this alterations, the single map display appears in red-yellow..
    I would like to use blue-green for displaying deactivations, but I do not know how to change in your script… I am sorry for my ignorance… !!
    So, if you have another suggestion…..
    Thanks in advance
    clarissa

  19. Nattou7
    October 27th, 2011 at 09:19 | #19

    Dear prof. Cui,

    I have a double-blind drug-placebo controlled study comparing the difference between groups in response to stress under the influence of drug/ placebo. Stress was administered one time before drug and one time after. SPM gives me values only when there are significant differences. For the second time stress task was administered, there was difference depending on the group type but Not the condition (drug/placebo). SPM indicates there is no significant difference, however, it does not give me any indication of the magnitude of activation in each group. I am asking the following: what does this “insiginificance” mean? It could be that both groups had very high activation magnitude that did not differ between them, or is it that the two groups simply dont have significant activation at all? Thank you so much for your constant help.

  20. October 27th, 2011 at 09:32 | #20

    @Nattou7
    It could be either. Sometimes both groups have nice activation but the “difference” between them is small and still insignificant.

  21. Malak
    October 29th, 2011 at 09:53 | #21

    @Xu Cui
    Dear Dr. Cui,

    How can I know which one of these scenarios is actually the case ? Anyway that SPM would be able to provide me with information about that?

    Thank you so much !!

  22. October 29th, 2011 at 20:05 | #22

    @Malak
    When you find A-B is not significant, you will have to do separate contrasts (A-baseline) and (B-baseline) to know which scenario is the case.

  23. May 16th, 2012 at 17:08 | #23

    What is sub-gyral in xjview and how is it defined? Not familiar with this term:)

  24. May 16th, 2012 at 21:12 | #24

    @Jacky Rongjun Yu
    I have no idea - the anatomical names are from standard database (TD and AAL).

  25. Hossam
    July 28th, 2012 at 19:19 | #25

    Dear Prof. Xu

    I would like to determine the excitation points in human brain ” or initial point of activation in human brain” ????? and how i can determine it in your tool in matlab??

    please prof. Xu, can you send to me your email address please ???

    Thank you so much !!

  26. July 28th, 2012 at 20:35 | #26

    @Hossam
    Simply click a voxel in the section view and the region name will be displayed.

  27. Hossam
    July 29th, 2012 at 03:17 | #27

    Dear Prof. Xu

    I need your assist in some points i couldn’t reach it:

    1. I want some papers talking about excitation points in human brain according to xjView tool, if you have .. can you send me the URLs, if you don’t .. can you tell me the word i must to use in search about these papers, or the method to reach it.
    ***********************************************************************
    2. According to any conditions you determine the excitation points in your brain model??? you choose it random or these points are known??
    ***********************************************************************
    3. I preparing a master in “visualization of the reaction diffusion in brain” .. my work about the propagation of excitation in human brain .. if you anything about this article please tell me
    ***********************************************************************

    please prof.xu assist me .. and can you make your answer in points like i mentioned please

    i am really thank you about your previous answer prof. xu, and i hope you give me your email to show you my works if you are interesting ..

    hossam_hussein@aast.edu

  28. July 29th, 2012 at 20:21 | #28

    @Hossam
    1. If you search xjview in google scholar you will find a bunch of papers citing xjview:
    http://scholar.google.com/scholar?hl=en&q=xjview&btnG=&as_sdt=1%2C5&as_sdtp=

    2. these points are known. I use wfu pickatlas database.
    3. Hossam, unfortunately I am not familiar with the field.

  29. September 12th, 2012 at 22:57 | #29

    xjview 8.10 is out.

  30. January 16th, 2013 at 13:52 | #30

    Currently it sounds like Movable Type is the best blogging platform available right now.
    (from what I’ve read) Is that what you are using on your blog?

  31. Lifang
    February 25th, 2013 at 19:44 | #31

    Dear Prof. Cui,

    I met a trouble and need your assist. After running a conjunction analysis based on SPM8, I view the processed image in Xjview, it appears to give some illogical thresholded p-values. i.e.,when setting p<.5, it always has the message “pValue is too small. No suprathreshold voxels.” This doesn’t make sense. Is there a reason for why this might happen, and/or is there a better way to handle this?

    Thanks in advance.
    Lifang

  32. Sugai Liang
    April 30th, 2013 at 07:57 | #32

    Dear Prof. Xu,
    I would like to know how to use xjview slice view to select the blobs figure. Where can I get the mannual about the xjview slice view?
    Thank you so much !!

  33. April 30th, 2013 at 08:51 | #33

    @Sugai Liang
    What do you mean by ’select the blobs figure’?

  34. Sugai Liang
    May 1st, 2013 at 02:13 | #34

    Dear Prof. Xu,
    Sorry. Afer the step of results in DARTEL VBM, some blobs can be seen in brain figures. And I would like to know how to use xjview slice view to select the blobs for paper illustration.
    Thank you!

  35. November 9th, 2015 at 13:04 | #35

    xjview 8.13 released
    http://www.alivelearn.net/?p=1781

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