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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)

严超赣学术报告_revised

 

学术报告
 
R-fMRI spontaneous low frequency fluctuations: making measurements more robust and a theoretical framework of the underlying electrophysiological “mechanisms”
 
报告人:严超赣 PhD
Research Scientist, Nathan Kline Institute for Psychiatric Research

严超赣学术报告

学术报告

 
R-fMRI spontaneous low frequency fluctuations: making measurements more robust and a theoretical framework of the underlying electrophysiological “mechanisms”
 
报告人:严超赣 PhD
Research Scientist, Nathan Kline Institute for Psychiatric Research

功能连接相关系数的t检验,需要对相关系数r取绝对值吗?

 各位老师好,
       我在做一个认知训练前后静息态功能连接改变的研究(ROI-wise),利用REST已经得到ROI之间的相关系数r以及经过r-z转换之后的z值,想利用z值做paired-t test(训练前vs训练后), 我想请教的问题是:如果我想看功能连接的强度是否因为认知训练发生改变,那么在得到相关系数r值之后需要对r值取绝对值吗?

Functional Connectivity 报错

用Rest计算FC时出错,是变量重名吗?需要如何修正?万分感谢!! 

Rest 1.8,MATLAB R2013a,win7(64bit)
 

Exception occured. (MATLAB:TooManyInputs)

Error using std (line 32)

Too many input arguments.

删除中间文件

 大家好。

用DPARSFAu预处理后,会生成很多中间文件。当被试很多的时候,太占硬盘空间。

对于功能像,每一步产生的文件都好理解,很容易删除不必要的中间文件。

对于结构像,有以下2个问题:

1. T1ImgCoreg,这个文件夹是否可以删除,而不影响后续 的处理?

2. T1ImgNewSegment , 里面有很多文件,哪些可以删除,而不影响后续的配准:

BiasField_T1.nii
c1T1.nii
c2T1.nii
c3T1.nii
c4T1.nii

删除中间文件

 大家好。

用DPARSFAu预处理后,会生成很多中间文件。当被试很多的时候,太占硬盘空间。

对于功能像,每一步产生的文件都好理解,很容易删除不必要的中间文件。

对于结构像,有以下2个问题:

1. T1ImgCoreg,这个文件夹是否可以删除,而不影响后续 的处理?

2. T1ImgNewSegment , 里面有很多文件,哪些可以删除,而不影响后续的配准:

BiasField_T1.nii
c1T1.nii
c2T1.nii
c3T1.nii
c4T1.nii

REST and DPARSF error on demonstration data set

I am using linux-Mint (ubuntu) system with MATLAB R2013b and SPM8. I could not get REST work at first place: it could not find subjects in the  ProcessingDemoData directory.

怎么利用这些ROI Signals呢?

 各位老师好:
      我用MICA提取了实验组的DMN网络(选择了Z-score转换),然后利用REST的extract ROI signals工具(感兴趣区选择为PCC/PC)提取的txt文件内容代表这个网络在这个ROI上的功能连接值,也是Z-value,理解的对吗?

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