Resting-State fMRI Data Analysis Toolkit plus V1.24 (RESTplus V1.24)

 
 
     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). 

     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 V1.24

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 V1.24 (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.

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.