Questions With This Site

  • Any questions you encountered with this site could be posted as a comment to this topic.
  • Please feel free to explore this researching site. I hope it be a start point of your resting-state fMRI research interest.

One advice is reading “How To Ask Questions The Smart Way”. And another advice may seem on the contrary: never hesitate to question yourself and then question in resting-state fMRI forum.

Re: Questions With This Site

I am new to re fMRI field. My analysis is simple: to assess and compare functional connectivity in 4 patient groups using 18 predetermined ROIs.
I ran REST- Functional Connectivity toolbox and got 1.) Pearson's r between each two ROIs within each group (FCmap.txt), 2.) z-transformed correlations for the same as 1.)(zFCmap.txt), and 3.) ROIFCmap.txt by group; what does this say exactly?: the functional connectivity among the individual ROI and all other predetermined ROIs within an individual patient?
How do I assess the statistical significance of 1.) and 2.)?

Perhaps dumb questions but it would help me a lot to know exactly what I am doing,
Thank you,

Re: Questions With This Site

 you should use z transformed correlaiton coefficient to perfrorm group analysis, that is zFCmap.txt which is pairwise correlation between ROIs. 

Re: Questions With This Site

Thank you for creating the freindly interface resting state fMRI. 
I want to calculate the cluster size using Rest AlphaSim. One of the input parameters is the mask file of the brain. My mask file is with '.mat' extension and the program doesn't allow it. Is it possible that you could convert the file to acceptable one for the rest program?

Thank you,

Re: Questions With This Site

 if your mask file in mat extension is indeed a brain with the same dimension as the REST template (i.e., matrix size is 61*73*61), you can use REST_WriteNiftiImage to write this mat file out into a nifti formated image file. 

The inputs for REST_WriteNiftiImage are:

1. Data: your mat file when you read it into matlab

2. Head: you can use [head data] = REST_ReadNiftiImage('one_of_the_image_file_you_want_mat_file_turns_to_be'); to get.

3. imageOUT: the path and name you want your new image file to be. 

Suppose if you had a different data dimension for your mat file from the common REST template file, you need to use REST ---> utilities --> image resampling to resample your generated image file to 61*73*61, 3*3*3 mm voxel size.



Calculating Functional Connectivity by Seed based Correlation Anlyasis...
Read 3D EPI functional images: "H:\Beijing-Nature\Patients\1\FunImgNormalizedSmoothedDetrendedFilteredCovremoved\sub001".??? Out of memory. Type HELP MEMORY for your options.
Error in ==> repmat at 104
    B = A(subs{:});
Error in ==> rest_to4d at 107
                    AllVolume =repmat(squeeze(AllVolume(:,:,:,1)), [1,1,1, nVolumn]);
Error in ==> y_SCA at 57
    [AllVolume,VoxelSize,theImgFileList, Header] =rest_to4d(AllVolume);
Error in ==> DPARSF_run at 1329
Error in ==> DPARSF>pushbuttonRun_Callback at 996
Error in ==> gui_mainfcn at 96
Error in ==> DPARSF at 48
    gui_mainfcn(gui_State, varargin{:});
??? Error while evaluating uicontrol Callback

Re: 用DPARSF跑数据,总是出错,求帮助


Re: 用DPARSF跑数据,总是出错,求帮助


Scrubbing Strategies

Dear DPARSF users and developers,

I have just started using this powerful toolbox and almost everything seems to be clearly explained and straightforward. I have only two questions.. Sorry, if they have already been asked - I didn't manage to find the answers on the forum.

I am currently running my analysis using DPARSF 2.3 (ADVANCED edition). In addition to ROI-based connectivity analysis, I'm planning to run Independent Component Analysis on *ARWSFB images using GIFT toolbox. I am not going to regress any nuisances, but will do scrubbing.

Here are my questions:
1. Which interpolation strategies would you generally recommend for ICA and/or ROI-based connectivity (Nearest Neighbor, Linear, Cubic Spline)?
2. What is the rationale behind removing 1 and 2 timepoints before and after "bad event", correspondingly, as recommended by default? Wouldn't we have a good control by removing just 1 and 1 instead?

Thank you very much in advance!

Regarding pre-processing of RS fMRI data

Hi all,

I am quite new to this field and now working on theanalysis of resting state data from healthy individuals.
I have tried using DPARSFA and I find it quite helpful.
Here are some questions regarding optimizing the pipe line.

  How to decide which bounding box to be specified for for Normalization? On what basis  is the default value chosen?

 What voxel size should be specified for Normalization?

What FWHM value should be set for smoothing? How is it  related  to the parameters set for Normalization?

Please help me..
Thanks in advance..

Re: Regarding pre-processing of RS fMRI data

 Bounding box: it will be OK if the bounding box is big enough to cover the entire brain.
Voxel size: usually a little bit smaller than the original sampling size. For example, original sampling size is 3.75*3.75*4 mm, the re-sampled size could be 3*3*3. 
Spatial smoothing: literature usually uses 4-8 mm. 

Re: Questions With This Site

Hi. I have a problem but it might be a Matlab problem. when I want to run slice viewer in rest it crashes in the moment of overlaying the reHo or the Alff results. When I Open REST I get the following message:

Warning: image_toolbox not valid
> In rest_sliceviewer>InitControls at 1053
  In rest_sliceviewer at 74
  In rest_sliceviewer at 38
  In rest at 153

I have added the Image_processing_Toolbox81_win64 to the patth but still not working. Any ideas?


Re: Questions With This Site

 Frist I feel so sorry that I did not response you timely .I suggest that you can try to use SPM to see whether the problem still exists.I think it may be better to consult the software R & D by Professor Yan Chaogang who will give you  informed answers


Re: Questions With This Site

I think his problem is the installation of imaging processing toolbox for MATLAB.
BTW, I am not a professor yet. :)

Re: Questions With This Site


Seems the image processing toolbox is not working. Or please re-install it by providing a license?









Re: 可以把6组看成不同的被试,不用session的那个,就是不

我想问老师一一分开具体是怎么做的呀?因为gift是以sub为单位打包压缩的,是把他们解压缩后,找到想要的component后,再做成文件夹吗?我用spm做one-sample t-test,用全脑做mask,没有发现任何voxel,到底是为什么呢?


做静息态数据统计分析的时候,是不是模板应该选择的尽量的小,这样在做AlphaSim的时候就能用更小的cluster size值做阈值?为什么我的结果用FDR校正的时候有阳性结果,而用AlphaSim校正后就基本没有结果了。是不是先验知识不足的情况下,AlphaSim校正更严格?如果我用一个比AlphaSim小的阈值做出了结果,能报出来吗?应该怎么报?




通常意义上的FDR校正是不考虑空间宽度的,而AlphaSim和Gaussian random field theory correction是需要考虑空间宽度的。









请高人指点如何查看rest slice view的结果?

小弟我试着做了统计,用rest slice view得出结果,但是看不懂结果,请高人指点下,非常感谢
# voxels structure(对于voxel structure,这个是否指16个相接的体素每个体素的部位?下表中如此分散,例如:左侧海马只有2个voxel BA34区就一个voxel,这些点有没有意义?)
3 Midbrain
3 Left Brainstem
2 Limbic Lobe
2 Hippocampus_L (aal)海马
2 ParaHippocampal_L (aal)左侧海马旁回前扣带回皮层
2 Parahippocampa Gyrus
2 Left Cerebrum
1 brodmann area 34前扣带回皮层
1 Gray Matter
Cluster 4
Number of voxels: 32
Peak MNI coordinate: 45 48 -15
Peak MNI coordinate region: // undefined // undefined // undefined // undefined // undefined // Frontal_Mid_Orb_R (aal)
Peak intensity: 3.9619(例如这个peak点在右侧额中回眶面,而右额中回有18个体素,右额中回眶面、额下回眶面分别有16个# voxels structure 和 15个体素,在报告结果时是否需要都报出来,还是只报右侧额中回眶面?其他脑区如BA11区怎么办?)
24 Right Cerebrum
21 Frontal Lobe
18 Middle Frontal Gyrus
16 Frontal_Mid_Orb_R (aal)右侧额中回眶面
15 Frontal_Inf_Orb_R (aal)右侧额下回眶面
6 brodmann area 11 额眶区(眶回,直回和上额回前侧的一部分)
6 Gray Matter
5 White Matter

Voxel masking

 Hello, I have some Resting state fMRI data an I want mask the voxels and use aal.but I dont know how to do?





Parametric test with GCA output

Dear REST experts,

Thanks for your recent works, REST-GCA :)
I am trying to perform granger causality analysis using REST-GCA. I conducted both coefficient-based and residual-based GCA for controls group and patients group and got several outputs for each group. These outputs were finally transformed into Z-value. Now, I'd like to perform between-group comparison using parametric test (i.e., two sample t-test). However, I am not sure what output files I use to do this.
(1) Is it right that two outputs ("GCA_x2y_1" and "GCA_y2x_1", which are not z-transformed values) for coefficient-based GCA are used to perform between-group comparison?
(2) Is it right that four outputs ("GCA_x2y_Transformed", "GCA_y2x_Transformed", "ZGCA_x2y_Transformed", and "ZGCA_y2x_Transformed") for residual-based GCA are used to compare both groups?

Please comments.
Thank you in advance.

请问一下用Dparsf选了DICOM to Nifiti以后,出现这个错误,是不是与原数据文件有关呢?

??? Undefined function or method 'spm' for input arguments of type 'char'.

Error in ==> DPARSF_run at 120

Error in ==> DPARSF>pushbuttonRun_Callback at 939

Error in ==> gui_mainfcn at 96

Error in ==> DPARSF at 41
gui_mainfcn(gui_State, varargin{:});

??? Error while evaluating uicontrol Callback





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