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Resting-State fMRI Data Analysis Toolkit plus V1.1 (RESTplus V1.1)


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 V1.1 (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)

time series of mean csf,WM

Dear Rest team

i would like to plot the time series of nuiscance regressors(CSF,WM,Global mean signal).i have  difficult of finding the time series of these regressors.i appreciate it if you can help me

regards

有没有做过fALFF与行为做过相关分析的,求matlab代码或类似代码!!!

我想做峰值点的fALFF与行为正确率的相关性,但是没有写过了类似的代码,各位能不能给点意见!!!

ALFF,ReHo信号与灰质结构信号的联系?

老师们好,按照臧老师文章的思路,我同时做了患者组的功能,结构的磁共振序列,患者组和对照组的全脑比较。

 

我把alff,reho,DKI的mk的t图空间标准化后,做了患者组和对照组的全脑比较。

静息态fmri数据如何与行为做相关???

正常人静息态fmri数据和行为准确率做相关。我先是fALFF做单样本t检验得出fALFF值显著高于全脑均值的部位,然后用该位置的fALFF值与行为准确率做相关,各位有没有做过类似的相关,求教!!!

MICA提取时间序列出错

求助!

脑功能连接数据处理精品入门培训班

主办单位:

   美德医疗
   中国科学院生物物理研究所北京磁共振脑成像研究中心

支持协会:

中国认知科学学会

ROI-wise得到的矩阵的值可以用来进行多因数分析吗?

我想做一个关于FC与其他因素的多因数分析,,FCMap可以转换成具体数值吗?

或者,我做差异脑区之间的ROI-wise,得到一个矩阵,,我可以用矩阵里面的数值代表这个差异脑区的功能连接值进行多因数分析吗?

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