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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. |
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: Resting-State fMRI Data Analysis Toolkit (REST, by SONG Xiao-Wei et al., http://www.restfmri.net).
Mail to Authors: SONG Xiao-Wei; YAN Chao-Gan; DONG Zhang-Ye
Multimedia Course: Data Processing of Resting-State fMRI
Submitted by admin on Sun, 12/13/2009 - 21:58 Permalink
fALFF GUI missed a F
A small bug encountered in Matlab 2009b:
fALFF GUI missed a F
in REST Version: 1.3, Release: 20091201