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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)

关于两种状态下的行为指标与ALFF/ReHo的相关分析 & xjview报道脑区

老师好,

   我做了一组被试(15人)在两种状态下(静息态和刺激态)的fMRI扫描,用paired t test做出两种状态的ALFF/ReHo差异脑区,然后提取差异脑区的ALFF/ReHo值,另外还测出每个被试分别在两种状态下的一个量表指标值(不算量表指标,是一个较客观的测试指标)。请问:

    (1)如果我要做这个指标值与差异脑区的ALFF/ReHo的相关性分析,以下三种方法哪种比较恰当:①只作刺激态下的指标值与刺激态下的ALFF/ReHo的相关分析;②分别作两种状态的指标值与ALFF/ReHo的相关分析,再进行对比;③把静息态和刺激态的数据串行放在一起(当作30人),再作指标值与ALFF/ReHo的相关分析?

对ALFF和fALFF结果的疑问

严老师:

      您好!我在对PD和正常对照组做双样本t检验后,ALFF能够出现正负激活区,但是在fALFF却没有结果,还有就是在用DPABI做完标准化以后的结果要比没有标准化的结果产生的信号范围大很多(基本上覆盖全脑),我对此很困惑,请老师指导,谢谢!

      祝好

关于用Rest做相关

各位大侠, 请教一下,在用REST做相关分析时遇到的问题:

我首先计算了ROI在治疗前后分别和全脑的相关,然后我想用治疗前后做Paired—t test的结果的差值来和临床做相关,我本来打算把这个差值的脑区作成一个mask,用Rest算这个功能连接的变化和临床变化的相关,不知道这种方法对不对?如果用这个方法的话,Rest功能连接这个Add Group Images 的地方应该加入那组数据呢?

非常感谢!

Re: Rat brain data

Hi

I downloaded your software and trying to run resting state for my data. Before that I would like to test your data, I was able to watch the video file on the animal data. Is there anyway I can download your sample data, to test it? Please let me know.

Thanks

Ned

GRF校正的疑惑

老师好,我投出去的ALFF的文章被拒了,一个reviewer说不太愿意接受alphasim的校正,如果要有,至少要clusters在100-200才可以接受。
我用FDR做了,没有结果。
但是用rest推荐的GRF的结果做出来的却非常不错,比alphasim的cluster大好多,每个cluster都在100以上了。
但是我有点疑问,是不是GRF的校正使用不太普遍? 我看到网上的文章大多使用alphasim或者FDR和FWE,GRF似乎只有不多的几篇。

GRF是可以被普遍接受的校正方法么?

请问REST里面的Image Calculator可以计算一张图像的平均值吗?

① REST image calculator可以计算一组图像的平均图像(mean(g1)),请问怎么计算一张图像的平均值吗?

② REST可以将一张T图转换成Z-score图吗?( i-mean(g1))/std(g1)这个计算的是i1相对于一组图的z-score图?如果我想把一个双样本t检验的T图转成Z图,请问怎么转?

谢谢老师!

对fmri数据怎么用FSL完成field map矫正?

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