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

33 sec read

xjView’s official webpage moves to https://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

第十九期 fNIRS Journal Club 通知 2021/05/29,9:30am

美国普渡大学童云杰助理教授,将为大家讲解他们组最近被接受的一篇使用近红外相位信息研究脑血流变化的文章。热烈欢迎大家参与讨论。 时间: 北京时间2021年5月29日上午9:30地点: https://zoom.com房间号: 846 8391 7517密码: 805190 童云杰教授简介:普渡大学 生物医学工程助理教授、博士生导师。主攻方向是多模态脑成像, 包括核磁,fNIRS, EEG。关注脑功能及生理信号的提取与研究。发表论文九十余篇,引用上千次(H-index = 20)。 童教授要讲解的文章如下: Liang Z, Tian H, Yang HC, Arimitsu T, Takahashi...
Xu Cui
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第十八期 fNIRS Journal Club 视频

北京时间2021年4月25日10点,北京师范大学的朱朝喆教授为大家讲解了他们最近几年在经颅脑图谱(Transcranial brain Atlas) 方面做的工作。视频如下: Youtube: https://youtu.be/EhYPuBPQ5uI Youku: 该视频在优酷上传后被优酷屏蔽,不清楚什么原因。申诉无效。
Xu Cui
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第七届全国近红外光谱脑功能成像学术会议

会议日期:2021年5月22日-24日会议地点:天津师范大学 一、 会议简介       近红外光谱脑功能成像(fNIRS)具有设备购买与使用成本低、可在自然环境条件下使用、具有较高的时间分辨率和空间定位能力等特点,受到了脑科学研究的高度重视。“近红外光谱脑功能成像学术会议”是由北京师范大学认知神经科学与学习国家重点实验室朱朝喆教授发起并组织的全国性学术会议。已连续成功举办六届,共吸引全国近百家高校、科研院所及医院的六百余名学者参加。该会议已成为国内规模和影响力最大的fNIRS脑成像学术活动。       本届会议由北京师范大学与天津师范大学联合主办。会议将延用往届会议将学术报告与研究方法工作坊相结合的模式。学术报告模块(5月22日周六)将邀请心理学与认知神经科学领域、基础与临床医学领域以及工程技术领域知名学者汇报其fNIRS最新研究成果;工作坊模块(5月23-24日)由fNIRS领域一线研究者系统讲授fNIRS成像原理、fNIRS实验设计、fNIRS数据分析与统计、fNIRS论文写作以及fNIRS前沿技术等。除理论讲授外,还设置了fNIRS空间定位与数据分析操作(NIRS-KIT软件)环节,此外还安排充足的研讨答疑时间以便与会人员交流互动。       具体日程与详细内容等最新消息请关注后续通知,可通过天津师范大学心理部网站http://psych.tjnu.edu.cn/或北京师范大学国家重点实验室网站http://brain.bnu.edu.cn/,或者扫描下方二维码关注微信公众号-“fNIRS脑成像实验室”查阅更新信息,期盼在天津师范大学与您相聚! 二、会议组织机构 主办单位:教育部人文社会科学重点研究基地天津师范大学心理与行为研究院、天津师范大学心理学部、北京师范大学认知神经科学与学习国家重点实验室会议主席:白学军、朱朝喆组织委员会:赵春健、杨邵峰、侯鑫、曹正操 三、说明1.        学术报告模块注册费:人民币500元/人;工作坊模块注册费:人民币2500元/人。发票为电子发票,内容均为:“会议费”。两个模块各自独立收费,参会者可根据自己需要进行选择。2.        注册费包括各自模块的资料费、午餐费;其他费用自理。3.        会议报告人免除会议模块注册费,其他费用请自理。4.       ...
Xu Cui
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39 Replies to “xjView, a viewing program for SPM2, SPM5, SPM8 and…”

  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. 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

  3. 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.

  4. @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

  5. 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?

  6. @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).

  7. 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?

  8. @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.

  9. 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

  10. @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

  11. 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).

  12. 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

  13. 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

  14. 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.

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

  16. @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 !!

  17. @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.

  18. 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 !!

  19. 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

  20. 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?

  21. 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

  22. 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 !!

  23. 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!

  24. Dear Dr. Cui

    Is there any way to use atlas which is not include in the software, for example:
    talairach-daemon-atlas. I have the .nii file from FSL data

    Thank you very much.

    xiaoxia

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