REST

<p>&nbsp;REST softwares.</p>

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: 

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: 

Resting-State fMRI Data Analysis Toolkit V1.7 (静息态功能磁共振数据处理工具包 V1.7)

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 and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, 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_V1.7_120101.

DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of REST V1.7 release 120101:
1. REST now support .nii and .nii.gz 3D or 4D files. (DONG Zhang-Ye and YAN Chao-Gan)
2. New module of Normality Test added at REST->Utilities->REST Normality Test. Please see an application in Zang, Z.X., Yan, C.G., Dong, Z.Y., Huang, J., Zang, Y.F., 2012. Granger causality analysis implementation on MATLAB: A graphic user interface toolkit for fMRI data processing. Journal of Neuroscience Methods 203, 418-426. (ZANG Zhen-Xiang)
3. Surface Map View Mode work with BrainNet Viewer (by Mingrui Xia, http://www.nitrc.org/projects/bnv). REST Slice Viewer->Misc->Surface View with BrainNet Viewer. Command line version: rest_CallBrainNetViewer.m or named to BrainNet_MapVolume.m in BrainNet Viewer. (YAN Chao-Gan)
4. The GUI view in Linux or Mac OS has been optimized. (YAN Chao-Gan)
5. Fixed a bug while frequency start with 0 or up to sampleFreq/2 in alff.m. (YAN Chao-Gan)
6. The coordinates conversion from Talairach space to MNI space has changed from tal2mni.m to tal2icbm_spm.m. The function is developed and validated by Jack Lancaster (Lancaster et al., 2007). The same for icbm_spm2tal.m. (YAN Chao-Gan)

Predefined Types: 

Resting-State fMRI Data Analysis Toolkit V1.6 (静息态功能磁共振数据处理工具包 V1.6)

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 and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, 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_V1.6_110505.

DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of REST V1.6 release 110505:
1. REST-GCA: provides a method that could transform the residual-based F into normally distributed Z score. For more details, please see http://www.restfmri.net/forum/REST-GCA. (ZANG Zhen-Xiang) 2. REST Image Calculator: Fixed an error when processing images of i10, i11.... and supporting keep "shift" key to select multiple groups or images. (DONG Zhang-Ye) 3. REST Slice Viewer: Fixed a bug in dispalying "only -" and a bug in dispaying unerlay with 2x2x2 voxel size. (DONG Zhang-Ye) 4. For defining ROIs, supporting keep "shift" key and select multiple mask files. From "Misc"->"Add multiple user-defined mask files". (DONG Zhang-Ye) 5. For extracting ROI signals, also support Multiple label values in a single mask file. 6. Fixed an error in the future MATLAB version in "[pathstr, name, ext, versn] = fileparts...".
New features of REST V1.5 release 101101:
1. Fixed a bug in rest_RegressOutCovariates_gui.m while processing multiple subjects with different covaribles in batch mode.

New features of REST V1.5 release 101025:
1. Module of Regional Homogeneity based on Coherence (Cohe-ReHo) has been added by LIU Dong-Qiang and DONG Zhang-Ye. For methodology, please see: Liu D, Yan C, Ren J, Yao L, Kiviniemi VJ and Zang Y (2010) Using coherence to measure regional homogeneity of resting-state fMRI signal. Front. Syst. Neurosci. 4:24. doi: 10.3389/fnsys.2010.00024.
2. In previous release of REST, removing covariates effects will also regress out linear trend. Now regressing out linear trend has been canceled in this step. Users can still regress out polynomial effects by using rest_regressOutCovariates.m in command line.
3. For rest_sliceviewer, fixed a bug of in displaying with MATLAB 2010 and support mouse wheel operation.
4. Fixed a bug in converting .nii files into NIfTI pairs (.img/.hdr).
5. Added new function of "corr(i1,i2,'spatial')" in REST Image Calculator.
6. Now can open a yoked structural image in displaying power spectrum.
7. Now can also pick up .nii files in GUI of reslice image.

Predefined Types: 

Resting-State fMRI Data Analysis Toolkit V1.5 (静息态功能磁共振数据处理工具包 V1.5)

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 and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, 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.

The latest release is REST_V1.5_101101.

DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of REST V1.5 release 101101:
1. Fixed a bug in rest_RegressOutCovariates_gui.m while processing multiple subjects with different covaribles in batch mode.

New features of REST V1.5 release 101025:
1. Module of Regional Homogeneity based on Coherence (Cohe-ReHo) has been added by LIU Dong-Qiang and DONG Zhang-Ye. For methodology, please see: Liu D, Yan C, Ren J, Yao L, Kiviniemi VJ and Zang Y (2010) Using coherence to measure regional homogeneity of resting-state fMRI signal. Front. Syst. Neurosci. 4:24. doi: 10.3389/fnsys.2010.00024.
2. In previous release of REST, removing covariates effects will also regress out linear trend. Now regressing out linear trend has been canceled in this step. Users can still regress out polynomial effects by using rest_regressOutCovariates.m in command line.
3. For rest_sliceviewer, fixed a bug of in displaying with MATLAB 2010 and support mouse wheel operation.
4. Fixed a bug in converting .nii files into NIfTI pairs (.img/.hdr).
5. Added new function of "corr(i1,i2,'spatial')" in REST Image Calculator.
6. Now can open a yoked structural image in displaying power spectrum.
7. Now can also pick up .nii files in GUI of reslice image.

Predefined Types: 

Resting-State fMRI Data Analysis Toolkit V1.4 (静息态功能磁共振数据处理工具包 V1.4)

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 and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, 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.

The latest release is REST_V1.4_100426.

DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of REST V1.4 release 100426:
1. Fixed a reading and writing bug of compatibility with SPM8.

New features of REST V1.4 release 100420:
1. In previous release of REST, there is a simple procedure for removing linear trend in bandpass filter (as fourier_filter.c in AFNI) regardless if detrend calculation has been performed before bandpass filter or not. Now this simple procedure for removing linear trend in bandpass filter has been canceled.
2. In previous release of REST, bandpass filter (or ALFF and fALFF) determined the frequency band a little smaller than the real wanted frequency band. For example, if the wanted band is 0.01-0.08, TR=2S, Time points=240, then the real wanted frequency band is 0.0104-0.07917, but the previous release of REST will determined to 0.0083-0.07708. This bug has been fixed in REST V1.4 release 100420. These two modifications will make the results obtained by REST V1.4 slightly different from those obtained by previous version of REST, please be careful.
3. REST Statistical Analysis: Statistical analysis module has been added -- One-Sample T-Test, Two-Sample T-Test, Paired T-Test, ANCOVA, and Correlation Analysis. The operations are much easier than the operations in SPM. Especially, the covariate images can be added into statistical analysis (such as adding GM volume images as covariates in statistical analysis).  (by YAN Chao-Gan)
4. REST Slice Viewer: Fixed a bug in displaying overlay with different bounding box from those of underlay. For example, if you use ch2.nii as underlay, but the bounding box of overlay is not [-90 -126 -72;90 90 108] (e.g. if you use SPM’s default: [-78 -112 -50; 78 76 85]), then REST Slice Viewer will display in a wrong way. Please re-display your image with REST V1.4 if your data with a bounding box different from [-90 -126 -72;90 90 108]. (by DONG Zhang-Ye)
5. REST-GCA: The Beta 1.0 release 100201 of REST-GCA supports only the signed-path coefficient maps at a fixed order=1 condition. In order to implement a more general GCA program, we updated REST-GCA. The updated version integrates two algorithms: the coefficient-based GCA and the residual-based GCA. The updated version supports any order. Please refer to http://www.restfmri.net/forum/REST-GCA for more details. (by ZANG Zhen-Xiang)

Predefined Types: 

Resting-state fMRI data analysis toolkit V1.3 (静息态功能磁共振数据处理工具包 V1.3)

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). You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, 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.

The latest release is REST2007V1.3_100201.

DOWNLOAD 

Multimedia Course: Data Processing of Resting-State fMRI

New features of REST V1.3 release 100201:
1. Modules added:
  (1) REST GCA 1.0 Beta: perform Granger Causality Analysis. Contributed by ZANG Zhen-Xiang, please see more details by clicking here
  (2) False Discovery Rate (FDR) Correction: under REST Slice Viewer / Misc Menu
2. Functions revised:
  (1) Make the outputname as 00001.img other than 1.img in REST Image Calculator.
3. Bugs Fixed:
  (1) Fixed a bug in ROI-wise functional connectivity calculation.

New features of REST V1.3 release 091215 (This release is updated by YAN Chao-Gan and DONG Zhang-Ye):
1. Modules added:
  (1) REST DICOM Sorter: sort and anonymize (optional) DICOM files.
2. Functions revised:
  (1) Adding more explanation of the correspondence between  x coordinates and Left/Right hemisphere when setting sphere ROI.
3. Bugs Fixed:
  (1) Fixed a bug in REST AlphaSim when rmm=6.
  (2) Fixed a bug in REST Image Calculator when creating output directory.
  (3) Fixed a bug that can not close the Utilities when quit REST.
  (4) Fixed a bug of displaying fALFF GUI in some Matlab versions (Missed a F, as Mr. SONG Xiao-Wei reported).

New features of REST V1.3 release 091201 (This release is updated by YAN Chao-Gan, DONG Zhang-Ye and ZHU Wei-Xuan):
1. Modules added:
  (1) REST AlphaSim: perform Monte Carlo simulation similar to AlphaSim in AFNI.
  (2) REST Image Calculator: calculate images, especially for group images.
  (3) Regress Out Covariates: regress nuisance covariates out.
  (4) Extract ROI Time Course: extract ROI time courses for multiple subjects.
  (5) Reslice Image: resclice images to a new vox size and new target space.
  (6) NIfTI nii to NIfTI pairs: convert NIfTI .nii (3D or 4D) files to NIfTI pairs (.hdr/.img) since REST only can process 3D .hdr/.img files.
2. Functions revised:
  (1) REST Slice Viewer: added P<->T, P<->F, P<->Z, P<->R conversion when threshoulding images; reading degree of freedom information from SPM statistical images; only+ and only-; save all clusters; cluster report functions; more AlphaSim thresholds (rmm=4, 5 and 6) for BrainMask_05_61x73x61.img; and make the Cluster Connectivity Criterion could be chosen among 6 voxels (surface), 18 voxels (edge) or 26 voxels (corner) according to rmm value.
  (2) ReHo: It should be noted that the previous release of REST does not calculate the ReHo value of the voxels near the border of the brain mask, i.e., any voxel of the 27 voxels in the cluster is outside the brain mask. The new release (here the closed test version) will calculate the ReHo value of the voxels near the border of the brain mask, users should be cautious when discussing the results near the border.
  (3) Functional Connectivity: Now it can process multiple subjects with different seed time courses (.txt) in batch mode. Give the seed time course configuration file as:
Seed_Time_Course_List.:
X:\Structural_Functional\Reprocess\Sub3Seed.txt
X:\Structural_Functional\Reprocess\Sub2Seed.txt
X:\Structural_Functional\Reprocess\Sub1Seed.txt
  (4) REST: Checking and fixing the error of reading and writing NIfTI images when REST starts
  (5) rest_to4d: If data has too huge or too many volumes, then it will be loaded into memory in 'single' format.
  (6) Templates: Added 3x3x3 AAL template and Brodmann template.
3. Bugs Fixed:
  (1) Fixed the bugs of color, montage and resize in REST Slice Viewer.
  (2) Fixed the bug of writing ANALYZE images.
  (3) Fixed the bug of writing data caused by finite in MATLAB 2009.
  (4) LastSphereMask would be stored under temp dir other than {REST_DIR} in case the users do not have write permission to {REST_DIR}.

Predefined Types: 

Resting-state fMRI data analysis toolkit V1.2 (静息态功能磁共振数据处理工具包 V1.2)

 

Resting-state fMRI data analysis toolkit V1.2 could be downloaded by click here. The latest release is 090101.

New features of REST V1.2 release 090101:

Predefined Types: 
Error | Forum of resting-state fMRI

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