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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)

静息态脑成像原理、方法与应用培训(第6、7期)第一轮通知

各位静息态脑功能成像研究同仁,广大脑功能研究领域的医生朋友们,杭师大认知与脑疾病研究中心组织举办的静息态脑成像原理、方法与应用培训又即将开班啦!

静息态脑成像原理、方法与应用培训已经在杭州成功举办了5届,学员们普遍反映每次都有新的收获,对各自的研究工作帮助也十分大。我们也是力求每次培训班都增加新的内容。 下两期培训班将于10月13-17日 (第6期),12月8-12日(第7期)举办,地点还是在杭州,培训讲师除了上几届的讲师外,还增加了万众瞩目的磁共振物理大牛、多模态脑影像专家、青年千人计划获得者、浙江省千人、杭州市钱江特聘教授王泽老师,期待他给我们带来的精彩讲座(内容见附件)。

培训班的培训时间、地点、培训内容、讲师介绍以及报名方法请见附件。

欢迎大家来杭州!

提取时间序列后进行小世界属性分析

 各位老师,我提取出了AAL90脑区的时间序列,通过corrcoef函数得到了相关系数矩阵,是否需要转换成z值后再进行小世界属性的分析?如何转换?

Slice timing error: Improper assignment with rectangular empty matrix.

I am trying to use DPARSFA to preprocess some .nii.gz files. I think for some reason the program is not detecting the time points correctly. If I leave the files as .nii.gz, the slice timing module will begin, and then give me this error (please continue reading after pasted content):

DPARSF中的filter

 各位老师,关于DPARSF中得filter,看到的解释是对于“静息态”通常研究低频段信号。那如果我是提取TASK的时间序列,还需要做filter吗?

关于预处理完的文件格式问题

 请教各位老师:
      为什么我用dparsf预处理完的文件格式有时候是nii,有时候又是img+hdr?

Three newly released toolboxes: ES Calc, TUMOR, Decom (all beta version), try and have fun!

I, on behalf of all contributors, would like to announce that three toolboxes are released for free downloading. All of them are Matlab-based, thus unzip and setpath is required (we encourage setpath SPM8, REST, DPARSF as well). For more details please see each toolbox's manual. These software are beta version v1.0, so please feel free to pose any comment, feedback, bug report, suggestions.

DPABI中DICOM Sorter出错

之前用REST分类DICOM数据出错,提示ProtocolName出错,试着在REST_DicomSorter.m中分别改成SequenceDescription和SequenceName之后运行还是出错。
之后在DPABI->Utilities->DICOM Sorter做相应修改(改成SequenceName)后再运行,出现一下报错:

??? Index exceeds matrix dimensions.

Error in ==> w_DCMSort at 15
    fprintf('Read %s etc.\n', OneDICOM{1});

AlphaSim矫正咨询

 各位老师好,我在使用SPM做双样本T检验的时候,explicit mask选用的是我的单样本T检验结果的并集MASK,这样的话最后双样本T检验的结果如果使用AlphaSim矫正的话,就不能直接使用REST slice viewer里面自带的那个表里的参数了吧?需要重新对我的并集MASK进行AlphaSim值进行评估,我想再问下如图中,在估计AlphaSim的时候这里的P值是什么意思?估计的时候需要改吗?

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