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)

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)

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.... (DONG Zhang-Ye)
3. REST Slice Viewer: Fixed a bug in dispalying "only -" and a bug in dispaying unerlay with 2x2x2 voxel size.
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. Fox Extracting ROI signals, also support Multiple label values in a single mask file. (DONG Zhang-Ye)
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.

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)

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}.

New features of REST V1.3 release 090525:

1. Fixed the bug of reading and writing error under the linux, unix or mac operation system.

New features of REST V1.3 release 090422:

1. The ReHo algorithm has been re-written to speed up the calculation of ReHo. The calculation time of one subject will reduced from about ten minutes to three minutes usually.
2. Fixed the bug of computing ReHo with 7 voxels or 19 voxels in a cluster.

New features of REST V1.3 release 090401: 

1. REST now can compute fractional ALFF.

2. Data in processing will not be converted to the format 'int16', and result data will be saved in the format 'single'.
3. Added "Correction Thresholds by AlphaSim" (under pull-down menu "Misc").
4. Fixed the bug of 'Set Overlay's Color bar' in Matlab R2007a or latter version which caused by the revision of imresize funtion in Matlab R2007a.

Thank Dr. CHENG Wen-Lian for some helpful works.

New features of REST V1.2 release 090101:

1. Now REST can support image saving function within rest_sliceviewer ("Save Image As" under pull-down menu "Misc").
2. The display mode of transverse multislices was changed as similar to AFNI in rest_sliceviewer.
3. Fixed the bug of cluster size threshold in rest_sliceviewer.
4. The default brain mask in REST was changed to new NIFTI mask which was the SPM5 apriori mask (brainmask.nii) thresholded at 50%. There were still two masks supported under the path \mask: white matter mask - SPM5 apriori mask (white.nii) thresholded at 90% and cerebrospinal fluid mask - SPM5 apriori mask (csf.nii) thresholded at 70%.

New features of REST V1.2:

1. REST V1.2 supports NIFTI (.hdr/.img) format now. Matlab 7.1 or above is recommended.

2. REST V1.2 can process multiple subjects with different covaribles in batch mode. Give the Covariables file as:
Covariables_List:
X:\Structural_Functional\Reprocess\Sub3Cov.txt
X:\Structural_Functional\Reprocess\Sub2Cov.txt
X:\Structural_Functional\Reprocess\Sub1Cov.txt

Setup instructions:
1. Download most recent REST2007V1.3_{date}.zip (such as REST2007V1.3_090401.zip) according to the date and extract it to a directory.
2. Add this directory to MATLAB's path.
3. Enter "rest" in the command window of MATLAB.
4. Enjoy the simple way to process resting-state fMRI data.

If you think REST is useful for your work, citing it in your paper would be greatly appreciated:
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

Mail to Authors: SONG Xiao-Wei; YAN Chao-Gan; DONG Zhang-Ye; ZANG Zhen-Xiang; ZHANG Han