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Forum of resting-state fMRI
欢迎到静息态功能磁共振成像论坛
Welcome to the forum of resting-state fMRI
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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)

DPARSF预处理报错

各位老师,晚上好。
我在用DPARSFA作数据预处理的时候报错如下,然后换了DPARSF还是一样的报错。但是单独用SPM8做头动校正又可以,实在不知道是哪里出了问题。
希望老师们不吝赐教,谢谢!

然后这是我的设定

用dparsf做FC时,总是报错,请教下老师

   用dparsf做FC时,总是报错matrix dimensions must agree,请问老师我应该怎么解决这个问题,这里的matrix 在哪个文件夹里,维数应该是多少?

DPASF报错,不明白是为什么,

 Converting T1 Images:Sub_001 OK

??? Undefined function or method 'file2mat' for input arguments of type
'struct'.
 
Error in ==> file_array.subsref>subfun at 80
t = file2mat(sobj,varargin{:});
 

有关REST-GCA对于任务态数据处理的问题

各位老师好:

我想用您开发的REST-GCA做任务态的GCA分析,可是看您的文献中提到rest-gca只适用于连续的任务态数据。我的数据不是连续任务态,是一很简单的组块设计的静息与任务等时相间的,并且我能很明确的把任务态的时间点全部提取出来,重新组成类似连续的任务态数据!不知道这样可不可以用rest-gca分析处理?此方法可行不可行?
望老师有时间给予解答与指导!谢谢!

DPABI出错

 下了DPABI用dparsf基本版出错,整个DPABI文件夹是add with subfolds添加进去的,matlab2013a,REST1.8,一点击Run就出错
Undefined function 'DPARSF_run' for input arguments of type 'struct'.

 
Error in DPARSF>pushbuttonRun_Callback (line 1109)
    [Error]=DPARSF_run(handles.Cfg);
 
Error in gui_mainfcn (line 96)

老师,请教一个有关静息态的问题

老师,我现在在用DPARSF做图像的处理。看您的视频中所做的有关功能连接的都是静息态的。
我们现在设计的是在一个视觉刺激下检测fMRI的BOLD像。请问在有事件刺激的条件下能做功能连接吗?需要额外测量静息态的图像作为参考吗?

老师,我用DPARSF做Slice Timeing时老报错,请问您是什么原因呢?

 
错误报告如下:
------------------------------------------------------------------------

Running job #1
------------------------------------------------------------------------
Running 'Slice Timing'
 

run DPABI

老師, 我這次run DPABI出現了以下錯誤
以往run DPARSFA都不會有的
是程式更新的關係, 還是哪個步驟出錯了呢
謝謝老師

Moving Coviables Removed Files:NL1507 OK
??? Index exceeds matrix dimensions.

Error in ==> DPARSFA_run>(parfor body) at 2672
MatFilename=[AutoDataProcessParameter.DataProcessDir,filesep,'T1ImgSegment',filesep,AutoDataProcessParameter.SubjectID{i},filesep,MatFileDir(1).name];

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