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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)

PCA教程

 各位老师好!
目前我想使用PCA软件分析静息态fMRI,但是不会用该软件,不知道那里有相关教程呢?
不甚感激!

关于resting state FC数据的相关分析问题

    各位老师好,我想请教几个关于静息态功能连接数据的相关分析的问题:
    

Problem of DPARSF v2.1

 Dear all, 

I have downloaded the test data from http://www.restfmri.net/forum/DemoData and load the configuration data DPARSF_Preprocess_ALFF_FC.mat by DPARSF v2.1 like below

Preprocessing by DPARSF v2.3

 Dear all, 
 
I have downloaded the test data from http://www.restfmri.net/forum/DemoData and do some preprocessing steps on Sub_001 by DPARSF v2.3. The first image of FunImg, A, AR, ARC, ARCW, ARCWS, ARCWSF are shown in order in the figure below.
 

How to get a mean grey matter map as a mask?

大家好,在阅读文献中,常看到这样的描述:
"The resulting T-map (or  Statistical map) was masked by a grey matter map, which was obtained by segmenting the mean normalized high resolution T1-weighted images of all the subjects, to include only the areas falling in grey matter."

我不确定自己理解的上述mask 做法是否正确,联系了作者,但暂时没有得到回复。故特此发帖与大家确定一下:

关于全脑信号回归

    各位老师好,本人在英文写稿过程中碰到了一个棘手的问题,想请教各位老师。在对rest state fMRI数据静息基于种子点的全脑功能连接分析时,我把全脑信号作为协变量进行了回归,但是单样本结果中的正负FC我都保留了,并进行正常组与病人组的组间比较。在讨论的写作过程中才发现对是否去除全脑信号的争议那么大,尤其我们的研究又纳入了负FC,而且在与病人行为学进行相关分析的过程中发现存在显著相关的为某个负FC。不知我们的结果这样采用了全脑信号回归能否继续成文,或者在文章能说明存在争议性就好了么,就怕到时会被审稿人抓住这个问题。希望能得到各位老师的解疑,谢谢!

REST中DICOM数据分类出现错误

老师:
     您好!我用的是matlabR2010b,安装在d盘,调用REST进行DICOM数据分类时出现以下错误,单个序列用SPM进行DICOM转成 NIfTI是可以进行。不知道什么原因造成REST报错呢?下一步怎么解决?
    谢谢!

错误提示如下:
     Now REST is Running on 0 workers.
Warning: Directory already exists.
> In rest_DicomSorter_gui>btnRun_Callback at 175

REST中DICOM数据分类出现错误

老师:
     您好!我用的是matlabR2010b,安装在d盘,调用REST进行DICOM数据分类时出现以下错误,单个序列用SPM进行DICOM转成 NIfTI是可以进行。不知道什么原因造成REST报错呢?下一步怎么解决?
    谢谢!

错误提示如下:
     Now REST is Running on 0 workers.
Warning: Directory already exists.
> In rest_DicomSorter_gui>btnRun_Callback at 175

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