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Resting-State fMRI Data Analysis Toolkit plus V1.2 (RESTplus V1.2)


RESTplus evolved from REST (Resting-State fMRI Data Analysis Toolkit). It is based on Matlab and SPM8. RESTplus includes four main modules, i.e., pipeline, statistical analysis, utilities and viewer.

     The pipeline (either fixed or flexible) module provides a very easy way for data processing. After arrangethe DICOM or NIFTI filesand click a few buttons to set parameters, the pipeline (or flexible) module will automatically calculate each processing step and give you all the processed data. The pipeline and flexible module can perform slice timing, realign, reorient, normalize, smooth, detrend, filter, nuisance covariates regression, Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), fractional ALFF (fALFF), Granger causality, degree centrality, voxel-mirrored homotopic connectivity (VMHC), and percent amplitude of fluctuation (PerAF). 


DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

 

     You can also use RESTplus to perform statistical analysis, 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, calculate intraclass correlation, perform quality assurance, normalize PET data, inverse data into original space, and sort DICOM files. RESTplus also includes ASL toolbox.

Contributor list:

     JIA Xi-Ze, Wang Jue, Liao Wei, Zhang Han, Liu Dong-qiang, Ji Gong-jun, Gao Zhong-zhan, Li Xun, Huang Hui-yuan, Wang Ze, Yan Chao-gan, Song Xiao-wei, Zang Yu-feng

New features of RESTplus V1.2 (released 20160202)

1  AlphaSim. The so-called "bug" has been fixed (the edge effects within the mask)

2 A bug for "Nuisance covariates regression" has been fixed

   For RESTplus V1.0 and RESTplus V1.1, the nuisance covariates regression result was wrong when two or more subjects were included (in pipeline or flexible module). For RESTplus V1.2, the bug of indir_RegressOutCov.m has been fixed (line30,line40).  If you have had any regression results from RESTplus V1.0 or RESTplus V1.1, you have to re-analyze your data with RESTplus V1.2. Sorry for the inconvenience.

3 A bug for help panel of "3d ASL Normalization" has been fixed.

1. AlphaSim. The so-called “bug” has been fixed in RESTplus V1.2.(the edge effects within the mask)
2. A bug for "Nuisance covariates regression" has been fixed
3. A bug for help panel of "3d ASL Normalization" has been fixed.
 
 

New features of RESTplus V1.1 (released 20160122)

1. SPM12 Compatible (JIA Xi-Ze)

2. Added ASL toolbox for pcasl and 3D ASL (WANG Ze and JIA Xi-Ze)

3. Updated rp_spm_write_vol.m and rp_spm_read_vols.m from SPM5 to SPM12 (JIA Xi-Ze and LI Xun).

4. Spatial correlation of images in Imaging Calculator, supporting mask selection (JIA Xi-Ze; Thanks the report by JIAO Fang-Yang).

5. Added standardized effect size for t-tests (GAO Zhong-Zhan and JIA Xi-Ze)

6. Fixed a bug when subject ID of dicom header includes ‘-’ or ‘:’. ‘_’ and ‘:’ will be replaced by ‘_’. (JIA Xi-Ze; Thanks report of LIU Yan)

 

Jia Xi-Ze, Wang Jue, Liao Wei, Zhang Han, Liu Dong-qiang, Ji Gong-jun, Gao Zhong-zhan, Li Xun, Huang Hui-yuan, Wang Ze, Yan Chao-gan, Song Xiao-wei, Zang Yu-feng.
   Jia Xi-Ze, Wang Jue, Liao Wei, Zhang Han, Liu Dong-qiang, Ji Gong-jun, Gao Zhong-zhan, Li Xun, Huang Hui-yuan, Wang Ze, Yan Chao-gan, Song Xiao-wei, Zang Yu-feng.

New features of RESTplus V1.0 beta release 151028:

1 Added pipeline module (JIA Xi-Ze)

2 Added flexible module (JIA Xi-Ze)

3 Added quality assurance module (JIA Xi-Ze)

4 Added REST inverse module (JIA Xi-Ze)

5 Added PET Normalize module (JIA Xi-Ze)

6 Added REST Intraclass correlation module (JIA Xi-Ze)

7 Added ASL toolbox for pasl (Wang Ze and JIA Xi-Ze)

8 fix a bug in of NIfTI nii to NIfTI pairs. (Li Xun and JIA Xi-Ze)

9 Nuisance covariates regression can add mean back (JIA Xi-Ze)

10 Module of percent amplitude of fluctuation (PerAF) has been added. (JIA Xi-Ze)

 

Thanks a lot for your email to JIA Xi-Ze (jiaxize@foxmail.com) for any suggestion.

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 DynamicBC1.2_20160415.  

Manual could also be downloaded here.

New features of DynamicBC 1.2 release 20160415: 

 

Fixed the step bugs when selecting window size.

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)

怎样获得默认网络的mask

请问各位老师,怎样获得比较准确的默认网络的mask?

关于ReHo

各位老师好,本人神内医生,刚开始学做fMRI,看了DPARSF视频,有点疑惑想请教。

Error in calling DPARSF

Hello!

I am trying to use DPARSF to preprocess my data. However, after opening DPABI when I click the DPARSF Basic Edition button, I'm getting this error message:

rest层现结果时voxel不在脑区内

各位老师,

  我在用rest看结果的时候会有出现异常增强或减低的voxels不在灰质上,在白质上,预处理的时候也是default mask,应该在哪一步如何做来去除这个因素。或者两样本t检验的时候将白质脑脊液成分做协变量?谢谢!

heatmap

 Can the authors provide representative fMRI raw data for both patient and control? Statistics and quantification are well done in the work, but some heatmap images of individual brain activities can make it more intuitive. 

双样本T检验的Alphasim校正

请教各位老师两个问题:

1.对双样本T检验进行Alphasim校正,是选用T检验的结果做为mask?还是选用什么文件作为mask?

2.在确定了cluster之后,在rest的Slice viewer中,输入的P值是输0.01还是输0.05?

谢谢各位老师赐教。

预处理的疑问以及功能连接校正方法

1,在1,在视频中,有关于去除头动较大的数据的问题,里面说的现在很多不在依据A标准(平动和转动大于多少mm)来作为排除标准,而是应用B标准(meanFD>0.2(Jenkinson))来作为排除标准,而我在实际预处理最后查看时发现用A标准排除的数据要比B标准排除的数据多,而且这个B标准我的理解是您说的Scrubbing这一步做的也就是您说的这一步一般在辅助材料里面写的。

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