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

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)

Paired t-test in dpabi with demo data

Hi there,
When I do 1 sample or 2 sample t-tests in dpabi with demo data it works fine but when I try paired t-test it produces following error:
Error using  .*
Array dimensions must match for binary array op.

Error in y_GroupAnalysis_Image (line 58)
MaskData = any(DependentVolume,4) .* MaskData; % skip the voxels with all
zeros

DynamicBC 中每个时间窗内设置多少个时间点可以被接受?

 各位老师,
       您们好!
       关于运用动态方法研究静息态功能磁共振数据,我想知道动态方法中的每个时间窗内至少需多少个时间点才算合理?有什么依据吗?
       还有,计算局部一致性,也至少需要多少个时间点才可以被接受?
       恳请各位老师帮忙解答,谢谢!

有关GCA计算结果的问题

  老师:

        您好!我最近首次初步学习GCA的计算!我的ROI采用的是Voxel Wise的方式,结果出来4种nii文件类型,分别有x2x,x2y,y2x,y2y,我想问一下这里的x和y分别对应的是什么?x就是指的我选的ROI吗?

有关GCA计算结果的问题

 老师:
        您好!我最近首次初步学习GCA的计算!我的ROI采用的是Voxel Wise的方式,结果出来4种nii文件类型,分别有x2x,x2y,y2x,y2y,我想问一下这里的x和y分别对应的是什么?x就是指的我选的ROI吗?

ICA相关知识

 张老师您好:

有几个问题想请教您:

Pdarsfa报错

我是新手,数据是Philips3.0采集的,TR2s,20层,150次采集,数据分析快到最后了老是报错,请求严老师给予指导,非常感谢!

Moving Dtrended Files:sub001 OK
Computing ALFF...
  Read 3D EPI functional images: "F:\Analysis\FunImgARCFD\sub001".

Pdarsfa报错

我是新手,数据是Philips3.0采集的,TR2s,20层,150次采集,数据分析快到最后了老是报错,请求严老师给予指导,非常感谢!

Moving Dtrended Files:sub001 OK
Computing ALFF...
  Read 3D EPI functional images: "F:\Analysis\FunImgARCFD\sub001".

rest做ROI-wise的FC时报错

DPARSF和rest分别是2.3和1.8 
(1)使用DPARSF预处理,在rest的FC中data directory选择DPARSF生成的FunImgNormalizedSmoothedDetrendedFilteredCovremoved文件夹,报错提示There's no data or non-data files in this directory

Syndicate content