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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_V1.1_20140710.  

Manual could also be downloaded here.

New features of DynamicBC 1.1 release 20140710:
1. Added the new utilties including the ‘Clustering’ and 'Spectrum' for dynamic FC/EC time series.
2. Added the new output of variance of dynamic FC/EC time series.  
 

New features of DynamicBC 1.0 release 20140429: 
This release fixed some minor bugs in dynamic FCD.

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)

静息态功能磁共振影像方法与应用培训班(REST南宁1511)通知

 静息态功能磁共振影像无创,并兼有较好的时间分辨率和空间分辨率,既可以检测脑局部活动进行精准定位,也可以揭示复杂的脑网络系统。静息态功能磁共振影像不仅具有很大的潜在临床应用价值,其“state”设计理念和计算方法也受到心理学家的重视。传统的静息态功能磁共振影像通常指BOLD技术,而随着成像技术与分析技术的进步,动脉自旋标记(ASL)除了提供脑血流的定量指标,还可以分析其时间序列的其它特征(如低频振幅、功能连接等等)。ASL与BOLD几乎可以同时获取,可以从不同的角度揭示生理、心理、病理状态的特征。

老师您好!我用dparsfa做预处理时总是报错?

 老师,您好!非常感谢您开发的一系列软件,给我们带来巨大的方便。我使用dparsfa做批预处理时总是出现如下错误,我试着把部分步骤去除,发现在最初的格式转化上也出现这种错误,不知道是怎么回事,希望得到老师解答,我用的是MATLAB R2014a,SPM8,我的具体参数设置如下图:

   谢谢老师!
  祝老师身体健康,工作顺利!
                                 学生:任靖远
Error using DPARSFA_run>(parfor body) (line 239)

question re multiple ROIs in functional connectivity

 Hi,

My name is Kathryn and I am new to REST toolkit but would like to use it for functional connectivity analyses and have encountered three problems.

REST Alphasim估计平滑,没有残差文件SPM.xVol.FWHM

 各位老师好!

 
 

Normallize 问题

给一个图像做Normalize,出错提示如下,图像在附件中,麻烦各位老师指教,多谢!

Running job #1
------------------------------------------------------------------------
Running 'Normalise: Estimate & Write'
Smoothing by 0 & 8mm..
Coarse Affine Registration..

    * - SPM8: spm_affreg  ----------------------------------------------

关于一篇reho文章的来自reviewer疑问

各位老师好,reviewer提了几个问题,但是其中有两个不知道怎么解释,能帮忙解答下吗?万分感谢!!!

DPARSF预处理报错

 老师您好,我再用dparsf做rest数据预处理时,一直提示错误:

Normalize-Write T1 Image:NC_Sub03_GuoYongLiang OK
Error using spm_bsplinc
File too small.
 
Error in y_Reslice (line 52)
C = spm_bsplinc(SourceHead, d);
 
Error in DPARSFA_run (line 2167)

出现了交互效应怎么处理

在做2*2的 ANOVA 分析(析因分析),影响因素为 分组(有病的,没有病的)和 基因型 (基因型 A和 B)

如果某个脑区  分组 或者 基因型的 主效应显著,解释起来很容易

如果某个脑区交互效应显著,该如何解释,在进一步统计分析时如何处理,麻烦各位老师指点

多谢大家!

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