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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)

关于小世界网络构建的问题

 各位老师:

DPARSF时报错,求原因

 各位老师:在用DPARSF处理数据时,出现下面的错误,不知是什么原因,期待各位老师的解答!祝好!

The following modules did not run:

Failed: Slice Timing
 
??? Error using ==> cfg_util>local_runcj at 1426

[DPARSF]extract AAL90 time series for making fc matrix

 各位同學老師好,

有一個問題想要請教大家,我利用DPARSF etract ROI TC時會產生一個ROITC的new folder看網路上可以將其中的ROICorrelation_FisherZ.mat (node數xnode數),可以作為放進NBS裡分析的data。我想要做一個AAL90一樣的fc matrix,但是extract ROI TC時得到的是90x(200x1)[AAL90x時間點]的mat檔,而不會得到FisherZ.mat,想請問我要如何將這樣的data做成或轉換成90x90的matrix呢?麻煩大家給我建議了,非常感謝!

How to find overlapping regions between various analyses?

 Dear Experts,

I have finished preliminary analyses in DPARSF including Reho, fALFF and degree centrality. These three analyses seem to overlap in certain brain regions, but it need to be further refined. My questions are:

PDARSF不读取数据,怎么办?

 各位老师大家好:
我在用DPARSF处理数据时,participants中总不能提取数据,不知是什么原因。重新在set path中安装DPARSF软件也不好使。把被试的功能像放在一个FunRaw的文件中了。
我用的是软件分别是D:\matlab\R2010b,REST1.8和DPABI1.1
原始文件是IMA格式,是否需要转化成DICOM格式的呢?若需要,怎么转化呢?
记忆中,DPARSF直接能提取IMA格式的文件。
期待各位老师的答复!
祝好!

voxel-wise GCA计算

 各位老师您好!

VBM analysis

 各位老师好!
请教下关于VBM全脑体积回归的老问题,在论坛里也搜索了,如果用VBMtoolbox分析的话,会有TXT文件,将三者值相加在统计的时候回归即可,
那么用DPARSFA中的NEW SEGAMENT+ DARTEL 做的时候,我不知道怎样找到有关的这样类似的文件,只有三个分割的图像,
我需要将图像“加起来”作为mask去回归吗? 具体怎么做呢? 非常感谢老师的解答!

從FunImg去跑一直出現錯誤

老師
為何我從FunImg去跑一直出現錯誤, 但卻可以FunRaw 開始

Generating voxel specific head motion for D:\analysis_CTL\regularup\new\RealignParameter\NL1967\rp_20121027_104943CO11LINYUEHCHINGs010a1001.txt...??? Undefined function or method 'gmdmp' for input
arguments of type 'double'.

Error in ==> y_VoxelSpecificHeadMotion at 79
Disp =
y_gmdmp(inv(M_RigidBodyTransform)*Head0.mat, 2,

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