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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)

关于动态FC及rsfMRI预处理的重采样问题

      各位老师好,投了篇关于rsfMRI的文章,内容是计算FC及其与行为学相关,审稿人问了两个问题,不知该如何回答,希望各位老师提点点子,或者有什么参考文献可循么?万分感谢!问题如下:
      

AlphaSim矫正咨询

各位老师好:
        我数据预处理的平滑是6mm,做完双样本T检验后,想使用AlphaSim矫正,首先利用REST软件进行平滑估计,统计图输入双样本T图,MASK选用的是一个灰质MASK(使用SPM自带的灰质模板卡了个0.3的阈值),估计出来的平滑总是很大(ReHo、alff、VBM的结果差不多都是这样)。。。这可能是什么原因造成的呢?

如何查看MRIdicom图像的参数。

各位老师:
     您们好!
     最近我导师给了一份被试数据,四个序列,用spm8查看只能看到3T 2D GR等信息,后面的TE、TR时间都看不到。请问还有什么别的方法可以导出dicom图像的各种参数吗? 

differences between images before and after covariates regression

老师,

您(们)好!

很想问问在 regress out 那些 covariates 后,为什么影像,无论脑内脑外都变化很大呢?比如,脑内外边缘开始变得不太清晰等等。

这些 residuals 应该是我们希望保留的。但很想明白为什么。

非常感谢!

关于使用DPARSF的几个问题。

各位老师们好,我在使用DPARSF过程中 有以下几个地方不明白,希望老师们能帮我解惑。
问题1,我在预处理时没有勾选 Extracting ROI time courses这几项,可是计算完fALFF后该Regress out nuisance covariates 时 就总报下列错误:(DPARSF设置如附件1所示)
 Read 3D EPI functional images: "E:\Analysis\FunImgNormalizedSmoothedDetrendedFiltered\Sub_001".

请教关于REST DC的问题

 请问老师,DC得出的结果zDC、mDC前缀各代表什么意思,DC positive binarized sum brain map和 DCpositive weighted sum brain map两个文件各代表什么意思?算统计时用哪个数据?

第十一届功能磁共振影像(fMRI)培训班:多模态fMRI技术及应用专题

第十一届功能磁共振影像(fMRI)培训班:多模态fMRI技术及应用专题

2014.12.11 – 12.14(中国·北京)  

 

联合主办单位: 

中国科学院生物物理研究所北京磁共振脑成像中心

中国科学院心理研究所磁共振成像研究中心

美德医疗

支持协会: 

中国认知科学学会

讲师单位: 

北京师范大学认知神经科学与学习国家重点实验室

Question: how to create ROI mask for functional connectivity?

Hi,

I am Grace. I am a beginner of the resting-fMRI analysis.
I want to use a user-defined ROI for a functional connectivity analysis.

I am wondering if you could tell me how to create ROI images with the MNI template using the REST gui step-by-step. 

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