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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)

inf in functional connectivity matrix

老师,

您好!

在得到 z 值化的FC matrix里,对角值因为计算都是 Inf。请问在后边的分析,比如网络分析里,需要把这个Inf换成1吗?还是直接保留它们在矩阵里也可以?

十分感谢!

任务态Event-related fMRI的试次个数怎么选择?

问各位老师一个问题:做Event-related fMRI研究时,试次的数量应该怎么选择?

DPARSF报错

数据整理没有问题一直报错如下,是怎么回事?
??? Index exceeds matrix dimensions.

 
Error in ==> DPARSFA_run>(parfor body) at 2224
        MeanFilename =
        [AutoDataProcessParameter.DataProcessDir,filesep,'RealignParameter',filesep,AutoDataProcessParameter.SubjectID{i},filesep,DirMean(1).name];

MATLAB 调用DPARSF 出现以下error

 Citing Information:

If you think DPARSF is useful for your work, citing it in your paper would be greatly appreciated.

ICA数据预处理

 请问做ICA之前的数据预处理要做nuisance covarites regression 吗?

FWHM and radius

 Hi everyone!!

I have a voxel size 2.5 2.5 4, how i set the FWHM and rmm in the REST alphasim?

Thank you!!!

DPARSFA回归WM,GM,CSF时生成的mask与Realign得到的图像的坐标不一致

老师:
您好!
我用DPARSFA对静息态的数据进行预处理,顺序是:SliceTiming-Realign-T1Segment-Nuisance Covariates Regression-Mormalize.遇到了两个问题:
1.我发现Nuisance Covariates Regression的时候生成的某些被试的白质、灰质、脑脊液、全脑信号mask的坐标位置与realign得到的图像的坐标位置有差异。如图(左侧为realignParameter文件夹内的图像,右侧为Masks中BrainMask图像,用MRIcro显示的同一坐标位置的截图):

经过VBM预处理和双样本t检验以后,想要利用统计出来的正负激活簇作为ROI来计算被试的这些ROI的体积,但是中间和后面出现了一系列问题

如题所示,我完全是这方面的小白,现在想要提取一些参数作为区分AD和NL,我手上只有结构型的MRI,所以用spm,rest这类工具有点茫然

现在我先是 通过VBM预处理,就是按照范丰梅写的那个《VBM处理流程-PDF》来的,经过了normalizing和segmenting,其中有的部分因为spm8和spm5有不同,所以我除了针对AD的预处理是thorough cleanup之外其他都是默认选项,比如那个high-demensional DATREL模板,最后使用了FWHM[8 8 8]的高斯平滑。

然后我选择了smwrp1*.nii这些文件用spm进行了双样本t检验,操作仍是参照范丰梅写的那个《VBM处理流程-PDF》.

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