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Dynamic brain connectome analysis toolbox


Dynamic brain connectome (DynamicBC) analysis toolbox is a Matlab toolbox to calculate Dynamic Functional Connectivity (d-FC) and Dynamic Effective Connectivity (d-EC). Sliding window analysis (Bivariate Pearson correlation and Granger causality) and time varying parameter regression method (Flexible Least Squares) are two dynamic analysis strategies for time-variant connectivity analysis in the DynamicBC. Granger causality density/strength (GCD/GCS) and functional connectivity density/strength (FCD/FCS) analysis would be performed in this toolbox. Add DynamicBC's directory to MATLAB's path and enter "DynamicBC" in the command window of MATLAB to enjoy it.

The latest release is DynamicBC_V1.0_140406.  

Manual could also be downloaded here.

Resting-State fMRI Data Analysis Toolkit V1.8 (静息态功能磁共振数据处理工具包 V1.8)

Resting-State fMRI Data Analysis Toolkit (REST) is a convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality, degree centrality, voxel-mirrored homotopic connectivity (VMHC) and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, perform Gaussian random field theory multiple comparison correction like easythresh in FSL, calculate your images, regress out covariates, extract ROI time courses, reslice images, and sort DICOM files. Download a MULTIMEDIA COURSE would be helpful for knowing more about how to use this software. Add REST's directory to MATLAB's path and enter "REST" in the command window of MATLAB to enjoy it.

Citation of REST is: 
Xiao-Wei Song, Zhang-Ye Dong, Xiang-Yu Long, Su-Fang Li, Xi-Nian Zuo, Chao-Zhe Zhu, Yong He, Chao-Gan Yan, Yu-Feng Zang. (2011) REST: A Toolkit for Resting-State Functional Magnetic Resonance Imaging Data Processing. PLoS ONE 6(9): e25031. doi:10.1371/journal.pone.0025031

The latest release is REST_V1.8_130615


DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of REST V1.8 release 130615:
1. Fixed a bug in temporal correlation of two groups of images in Image Calculator. (Thanks for the report of ZHANG Han)

2. The midline of VMHC results were set to zero. (YAN Chao-Gan)
 

New features of REST V1.8 release 130303:
When calling Mingrui Xia's BrainNet Viewer (http://www.nitrc.org/projects/bnv/), the default surface template is changed to the smoothed version (BrainMesh_ICBM152_smoothed.nv). The previous default template (BrainMesh_ICBM152.nv) hide more information in the sulcus. If the users want to use BrainMesh_ICBM152.nv as default surface template, please uncomment Line 3740 in rest_sliceviewer: %SurfFileName=[BrainNetViewerPath,filesep,'Data',filesep,'SurfTemplate',filesep,'BrainMesh_ICBM152.nv'];
(After discussion with Mingrui Xia).

New features of REST V1.8 release 130214:
1.    This release fixed some minor bugs, will not affect any data analysis.
2.    Fixed a bug when using .nii(.gz) files in REST Image Calculator. (WANG Xin-Di)
3.    Fixed a bug in using .nii(.gz) files in GCA analyses. (ZANG Zhen-Xiang)
4.    Fixed the imresize_old bug of REST Slice Viewer with Matlab 2012b. (YAN Chao-Gan)

New features of REST V1.8 release 121225:
1.    Support parallel computing! If you installed the MATLAB parallel computing toolbox, REST can distribute the subjects into different CPU cores. (WANG Xin-Di and YAN Chao-Gan).
2.    Algorithm change: (1) Filtering: a separate function for matrix filtering was written. The low cutoff frequency index calculation changed from round (in REST V1.7) to "ceil". E.g., if low cut off corresponded to index 5.1, now it will start from 6 other than 5. This change also applies to ALFF and fALFF calculation. The filtered data changes slightly, about 0.0001. (2) The ALFF generated by the new version is sqrt(2/N) times of the original version. (new version used: 2*abs(fft(x))/N; original version used:  sqrt(2*abs(fft(x))^2/N)). This change will not affect group analysis (as each individual scaled the same number), and will not affect mALFF and fALFF calculation as this factor will be normalized. (3) In the calculation of ReHo, the rank will keep as double and no longer converted into uint16, thus created slight difference with REST V1.7. (YAN Chao-Gan)
3.    REST Slice Viewer support 4D file display and the maximum and minimum value could be set. (WANG Xin-Di)
4.    Gaussian random field (GRF) theory multiple comparison correction (like easythresh in FSL) was supported. The smoothness could be evaluated for GRF correction or AlphaSim correction. (GUI by WANG Xin-Di, algorithm by YAN Chao-Gan)
5.    Modules of voxel-mirrored homotopic connectivity (VMHC) (Zuo et al., 2010), Degree Centrality (Buckner et al., 2009) were added. (GUI by WANG Xin-Di, algorithm by YAN Chao-Gan)
6.    REST GCA: could handle multiple ROIs (other than 2) in ROI-wise GCA now. Fixed a bug of discordance between the outputs and the description in REST-GCA readme in the pre-release of REST V1.8. (ZANG Zhen-Xiang)
7.    rest_readfile.m and rest_writefile: The default format changed to .nii from .img. (WANG Xin-Di)
8.    rest_to4d.m: now support one 4d file other than a directory, also support a cell of image filenames. (YAN Chao-Gan)
9.    rest_regress_ss.m: add the output of T value. (YAN Chao-Gan)
10.    rest_Write4DNIfTI.m: This function was added for write 4D nifti files based on SPM’s nifti function. (YAN Chao-Gan)
11.    rest_writefile.m: No longer need to change to RPI before writing. (YAN Chao-Gan)

启动rest时出现警告

 请教老师,我启动rest时总是出现下面警告,是怎么回事?

关于DPARSF处理数据中间环节出错

 老师们好,我有几个问题想请教大家。
1、在DPARSF跑数据中,detrend这一步出错,Warning: Invalid escape sequence appears in format string. See help sprintf for valid escape sequences.

> In rest_detrend at 24
  In DPARSF_run at 992
  In DPARSF>pushbuttonRun_Callback at 976
  In gui_mainfcn at 96
  In DPARSF at 43

目前有病人组前后两次的静息态MRI数据和健康对照组的静息态数据,请问怎样进行统计呢?

 我们对病人组在治疗前后均扫描了静息态数据,也采集了健康对照组的静息态数据,在对ALFF用REST统计上犯了难,目前的试了一下,我的步骤和问题如下:
1.病人前后和对照共三组数据做ANOVA,得到了一个脑区,再在这个脑区内用REST做两两比较(该脑区为mask),发现病人治疗前该脑区内大部分voxel比对照高(REST双样本T检验),而治疗后该脑区大部分voxel比治疗前更高(用了REST的配对T检验),但是治疗后的影像与对照比却没有得到阳性发现(REST双样本T检验,跟前面是同样的多重比较矫正水平),对于这一点我就觉得纳闷,为什么治疗前比对照高,治疗后更高,治疗后比对照反而没有影像学的阳性发现?
2、我也知道不是独立样本不适合做配对T检验和ANOVA,但是有什么更合适的办法吗?或者现在我的方法有没有可以被接受的可能?

做GCA是否要选择去除协变量的数据

各位老师,同学好。

我现在在做GCA,用去除协变量的数据和用filtered的数据(不去除协变量)分别作了,结果不同,想知道应该用那个数据做呢,哪个更可靠呢。

谢谢。

请教各位老师是不是循环分析的情况?

各位老师,同学好~
我的实验做出了两组样本脑体积有差异的脑区,然后我想提取这些脑区的平均信号强度来与一组临床评分做相关分析,目的是想了解这些有差异的脑区与临床评分的相关性如何。
我的问题是:
1. 现在已知两组病人的临床评分组间无差异,在这种情况下,我是否可以将两组病人的图像合在一起与评分做相关?自己觉得组间评分如果有差异,再与有差异的脑区做相关才会有double dipping的嫌疑,不知道我理解的对不对?还想听听各位老师的意见

2. 或者我将有差异的脑区的平均信号强度分组来做相关。也就是说A组的信号和A组的评分,B组的信号和B组的评分各自做相关,然后在结果讨论的时候就分别对两组病人讨论。看的文献这么做的不多,不知道方法学上有没有不妥?如果分开做的话,那就是做两次相关,结果我需要P/N吗?

Undefined function or variable ‘file array’

              I'm fresher to REST Toolbox. Recently, I use it to compute ALFF. Unfortunately, At first step, it cause an error and promt “Undefined function or variable ‘file array’ ”.
              I tried to find the origin by baidu or google but failed. I think it stemed from wrong data format. The data format used is NIfTI 3D hdr/img pairs which were transformed from nii by MRIcro. My specific setting is "WIN7, REST1.8,MATLAB 2012b". 
             Can anyone solve this ERROR? And tell me how to do next. Thank you !

 

关于Alphasim校正

 各位老师好,最近投稿遇到审稿人建议不使用Alphasim校正,但是FDR/FWE校正又不survive,请问有什么办法能解决,可不可以先取uncorrected p< 0.05的mask内做spm small volume,以达到FDR校正? 谢谢老师! 

关于两样本t检验统计的AlphaSim校正问题

 关于两样本t检验统计的AlphaSim校正问题,想向各位老师请教:

Reviewer给我的Comments是:

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