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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)

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?

DPARSFA

Hi,
I'm using demo data and DPARSFA. When I choose my working directory (which has two folders FunRaw and T1Img) it does not pick up participants. But when I run then it shows. Can you tell me what's going on? If I use basic edition of DPARSF it picks up correctly.
Thanks,
Pritha

DPARSF Advanced版本无法找到participants,手动添加也找不到,而basic能找到是怎么回事

 各位专家,我想询问下为什么刚刚下载的DPARSF来处理ProcessingDemoData,进入Advanced版就无法读取participants右键添加也找不到,而basic版能自动找到,是怎么回事呢?
数据文件按视频说的存在了F/Analysis/FunRaw
                                                     T1Raw

overlay result images to check regional overlap among different analyses

Dear experts,

I have finished running the Reho and fALFF in DPARSF. The brain regions that have significant group differences (patients vs healthy controls) seem overlap between Reho and fALFF. I would like to take a closer look at these results, but slice viewer can only have one overlay at a time. Is there any way/script that would help to overlay more than one statistical images on top of each other in Rest or Brainnet viewer?

thank you very much!

Jie

ALFF反映的是状态还是特质?

 各位老师好!
      我最近用ALFF与某个心理变量之间的关系进行了分析,得到了一些脑区的ALFF值与某个心理变量有关。有审稿专家说ALFF反映的是状态的变化,问得到的结果反映的到底是状态上的关系还是特质上的关系。所以,我想请教各位老师:ALFF真的只是反映了状态的变化吗?与特质有没有关系?先提前感谢您在忙碌之中的回答!

使用DPARSF做任务态fMRI图像预处理报错

各位老师,大家好!
想使用DPARSF做预处理,数据是4组,每组20人,每个人有2个run。我将每个人的每个run给予独立的命名,如sub_001_run1,sub_001_run2,整理存入FunRaw。再将每个人的3dT1相数据整理存入T1Raw文件夹下对应的sub_001_run1。复制一份存入sub_001_run2。由于是任务态的数据,我只想做realign,normalize by using segment T1 ,smooth。

DPARSF中我只选择了:EPI DICOM to NIFTI,Realign,Reorient Fun*,T1 DICOM to NIFTI,Affine Regularisation in Segmentation,Normalize,smooth

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