Resting-state fMRI topics

Resting-State fMRI Data Analysis Toolkit plus V1.29 (RESTplus V1.29)

 
 
 
     RESTplus 从 REST(静息状态 fMRI 数据分析工具包)演变而来。它基于 Matlab 和 SPM8。RESTplus 包括四个主要模块,即管道、统计分析、实用程序和查看器。

     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). 

     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.

 

DOWNLOAD RESTplus V1.29

X.-Z. Jia, J. Wang, H.-Y. Sun, H. Zhang, W. Liao, Z. Wang, C.-G. Yan, X.-W. Song, Y.-F. Zang, RESTplus: an improved toolkit for resting-state functional magnetic resonance imaging data processing. Science Bulletin. 64, 953–954 (2019). doi:10.1016/j.scib.2019.05.008
An example of RS-fMRI data analysis using RESTplus
Multimedia Course: Data Processing of Resting-State fMRI 

Contributor list: JIA Xi-Ze,Sun Jia-Wei, Li Zi-Qi, Yuan Li-Xia, 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 V1.29(released 20240308)

1、Added Temporal Dynamic PerAF Analysis (Volume-based). 

 

New features of RESTplus V1.28(released 20230706)

1. Fixed a bug where the file path with ".nii.gz" as a suffix was read

 

New features of RESTplus V1.27(released 20220829)

1. Fix the problem that the mask vaule is 1 while that of the NIFTI data is 0 in some voxels in two sample t-test.

 

New features of RESTplus V1.26(released 20220820)

1. Upgraded the data type of NIFTI Header to 32 bit float. 

 

New features of RESTplus V1.25 (released 20210630) 

1. Added a plug-in to obtain DICOM information of functional image in bluk.

2. Compatibility with Mac system was improved.

3. Added the function which can obtain information of Slice Order automatically.

4. Added a tool to delete time points from back to front in bluk.

5. Images Flip was added.

6. Upgraded the FD module, the new version will automatically generate the Mean FD indicator for each subject.

7. Upgraded statistics module. The new version can estimate FWHM based on residual error and apply it to GRF correction.

8. Upgraded the function of converting DICOM format to NIFTI (the new version is based on: dcm2niix.exe) .

9. Upgraded the GRF correction module. The new version can save both T and Z maps at the same time.

10. Added code of making intersection mask.

 

New features of RESTplus V1.24 (released 20200902) (Sun Jia-Wei, Li Zi-Qi, Jia Xi-Ze) 

1. Added SSM-PCA in Statistical Analysis Module. (Yuan Li-Xia)

Please see more details about SSM-PCA at: Yuan LX, Wang JB, Zhao N, et al. Intra- and Inter-scanner Reliability of Scaled Subprofile Model of Principal Component Analysis on ALFF in Resting-State fMRI Under Eyes Open and Closed Conditions. Front Neurosci. 2018;12:311. Published 2018 May 25. doi:10.3389/fnins.2018.00311

2. Added an approach “Using T1 image new segment” in normalization.

3. Rigid-body 6 parameter model was replaced by Friston 24-parameter model in “Nuisance covariates regression”. 

Citation: Friston KJ, Williams S, Howard R, Frackowiak RS, Turner R. Movement-related effects in fMRI time-series. Magn Reson Med. 1996;35(3):346-355. doi:10.1002/mrm.1910350312.

4. RESTplus V1.24 is compatible with Matlab2018a now. 

5. Added Temporal Dynamic Analysis (Volume-based). 

6. Added Mixed Effects Analysis in Statistical Analysis Module.

7. Fixed a bug about the settings of “User defined mask” in pipeline.

8. Fixed a bug which was appeared when the user name was in Chinese. The error was about the file called 'Img4Chek.img' that was generated in User Folder in normalization.

9. Fixed a bug that was caused by selecting multiple ROI paths in ROI wise Functional connectivity.

 

New features of RESTplus V1.23 (released 20200428)

1. Added Wavelet-ALFF module. (Sun Jia-Wei,Jia Xi-Ze)

2. If 'not add mean back' and 'PerAF' are selected at the same time,a tooltip will be generated. (Sun Jia-Wei,Jia Xi-Ze)

3. The settings of TR and Smooth are fixed. (Sun Jia-Wei,Jia Xi-Ze)

4.‘Save Clusters’is fixed to display both positive and negative associations on the viewer after saving all the clusters. (Li Zi-Qi,Jia Xi-Ze)

 

New features of RESTplus V1.22 (released 20190420)

Add BDA module. (Jia Xi-Ze)

 

New features of RESTplus V1.21 (released 20190205)

Add mean back modification (Wei Wei)

 

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.

RESTplus V1.0 beta release 151028 新特性:

1 增加流水线模块(贾熙泽)

2 新增灵活模块(贾熙泽)

3 增加质量保证模块(贾熙泽)

4 增加 REST 逆向模块(贾熙泽)

5 新增PET归一化模块(贾熙泽)

6 增加 REST Intraclass 关联模块 (JIA Xi-Ze)

7 新增pasl的ASL工具箱(王泽和贾熙泽)

8 修复了 NIfTI nii 到 NIfTI 对的错误。(李迅、贾熙泽)

9 Nuisance covariates regression can add mean back (贾熙泽)

10 增加了波动幅度百分比(PerAF)模块。(贾熙泽)

 

非常感谢您给贾熙泽 (jiaxize@foxmail.com) 的任何建议。

Predefined Types: 

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 DynamicBC2.2_20181112

Manual could also be downloaded here

New features of DynamicBC 2.0 release 20180311:
New features of DynamicBC2.2 release 20181112:
--Added a visualization module for connectogram.
--Added a demo for visualization a connectogram.
--Added new feature for cluster number estimation.
--Fixed a bug for clustering the ALFF maps.

 

New features of DynamicBC 2.0 release 20180311:
   --Fixed minor bugs in the Clustering module.

New features of DynamicBC 2.0 release 20171228:
1. Changed the toolbox cover.
2. Added the new module for dynamic intrinsic brain activity (dynamic ALFF).  

 

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)

Predefined Types: 

Centroid and Median cluster?

I am utilizing the DynamicBC k-means clustering algorithm and have encountered a file called the "Centroid", which is matrix that exhibits smaller values in comparison to the Median cluster. I am interested in understanding the underlying reasons for this discrepancy and determining which of these metraces, Centroid or Median cluster, is more appropriate for my analysis. Additionally, I would appreciate an explanation of the concept of "pCentroid" as well, which is in the same directory as the Centroid.

关于预处理的一个疑惑

各位老师好,在预处理的过程中,我DPARSFA---V5,calculate in MNI space 这个预处理流程,有一点小疑问,这个流程勾选了Extract ROI time courses,如果我并没有Define ROI,是不是就代表提取了所有脑区的时间序列呢?
然后在这个基础之上,我只要第二步进入DPARSFA---勾选Functional Connectivity,再Define自己想要的脑区,就可以获得ROI到全脑的功能连接了。这样对吗?

如何通过dpabi的NBS方法对一组被试的功能连接的连边进行年龄效应分析(不是组间比较,而是进行连续变量分析)

老师们好:
我有一组被试的功能连接矩阵,我想通过NBS分析哪些连边随着发育增强,哪些减弱,同时把性别和头动作为协变量。
我没有对被试进行分组比较,而是想观察哪些边随着年龄的增长有显著的变化。
那么:
(1)在dpabi的Statistical Analysis界面的第一个下拉框里面应该选哪个呢?
(2)在Text Covariates里是放入age, sex, mFD三个协变量,还是只放入sex和mFD两个协变量呢?
(3)最后在哪个生成的文件里给出age的效应呢?
谢谢老师们!
祝生活愉快~

REST compatibility with MATLAB

Hello everyone,

I have MATLAB R2016a installed, and I've been trying to get the latest versions of REST to work on it (REST_V1.8_130615), unfortunately with no success so far.

Does anybody know what version of MATLAB is the latest version of REST compatible with?

Thank you for your help!
Robin

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