Forum of resting-state fMRI 欢迎到静息态功能磁共振成像论坛 Welcome to the forum of resting-state fMRI en Resting-State fMRI Data Analysis Toolkit plus V1.2 (RESTplus V1.2) <table border="0" cellpadding="1" cellspacing="1" width="0"> <tr> <td width="520"><br><img align="middle" alt="" src="/forum/sites/default/files/users/zhuhailong/image/restplus1.1.png" style="width:508px; height:450px"></td> <td> <p><span lang="EN-US" style="font-family:Calibri, sans-serif; font-size:15px">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.</span></p> <p><span lang="EN-US">&nbsp;</span><span style="font-family:Calibri, sans-serif">&nbsp; &nbsp;&nbsp;</span><span style="font-family:Calibri, sans-serif; font-size:15px">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).</span><strong>&nbsp;</strong></p> <p><br><strong><span><a href=""><span>DOWNLOAD</span></a></span></strong><span><span><strong>&nbsp;</strong></span></span><br><br><span><strong> </strong></span><a href=""><span><strong>Multimedia Course: Data Processing of Resting-State fMRI</strong></span></a><br><span> </span></p> </td> </tr> </table> <div> <div>&nbsp;</div> <p><span>&nbsp; &nbsp; &nbsp;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.</span></p> <p><span style="line-height:20.4px">Contributor list:</span></p> <p>&nbsp; &nbsp; &nbsp;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</p> <p>New features of RESTplus V1.2 (released 20160202)</p> <p>1 &nbsp;AlphaSim. The so-called "bug" has been fixed (the edge effects within the mask)</p> <p>2 A bug for "Nuisance covariates regression" has been fixed</p> <p>&nbsp; <span style="color:#f00">&nbsp;</span><span style="line-height:20.4px"><span style="color:#f00"><strong><span style="background-color:#ffff00">For RESTplus V1.0 and RESTplus V1.1, the nuisance covariates regression result was wrong </span></strong></span>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). &nbsp;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.</span></p> <p>3 A bug for help panel of "3d ASL Normalization" has been fixed.</p> <div style="position:absolute; top:785.141px; width:1px; height:1px; overflow:hidden">1. AlphaSim. The so-called “bug” has been fixed in RESTplus V1.2.(the edge effects within the mask)</div> <div style="position:absolute; top:785.141px; width:1px; height:1px; overflow:hidden">2. A bug for "Nuisance covariates regression" has been fixed</div> <div style="position:absolute; top:785.141px; width:1px; height:1px; overflow:hidden">3. A bug for help panel of "3d ASL Normalization" has been fixed.</div> <div> <div>&nbsp;</div> <div>&nbsp;</div> </div> <p>New features of RESTplus V1.1 (released 20160122)</p> <p>1. SPM12 Compatible (JIA Xi-Ze)</p> <p>2. Added ASL toolbox for pcasl and 3D ASL (WANG Ze and JIA Xi-Ze)</p> <p>3. Updated rp_spm_write_vol.m and rp_spm_read_vols.m from SPM5 to SPM12 (JIA Xi-Ze and LI Xun).</p> <p>4. Spatial correlation of images in Imaging Calculator, supporting mask selection (JIA Xi-Ze; Thanks the report by JIAO Fang-Yang).</p> <p>5. Added standardized effect size for t-tests (GAO Zhong-Zhan and JIA Xi-Ze)</p> <p>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)</p> <p>&nbsp;</p> <div style="position:absolute; top:661.969px; width:1px; height:1px; overflow:hidden">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.</div> <div style="position:absolute; top:535.188px; width:1px; height:1px; overflow:hidden">&nbsp; &nbsp;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.</div> </div> <p><span>New features of RESTplus V1.0 beta release 151028:</span></p> <p><span>1 Added pipeline module (JIA Xi-Ze)</span></p> <p><span>2 Added flexible module (JIA Xi-Ze)</span></p> <p><span>3 Added quality assurance module (JIA Xi-Ze)</span></p> <p><span>4 Added REST inverse module (JIA Xi-Ze)</span></p> <p><span>5 Added PET Normalize module (JIA Xi-Ze)</span></p> <p><span>6 Added REST Intraclass correlation module (JIA Xi-Ze)</span></p> <p><span>7 Added ASL toolbox for pasl (Wang Ze and JIA Xi-Ze)</span></p> <p><span>8 fix a bug in of NIfTI nii to NIfTI pairs. (Li Xun and JIA Xi-Ze)</span></p> <p><span>9 Nuisance covariates regression can add mean back (JIA Xi-Ze)</span></p> <p><span>10 Module of percent amplitude of fluctuation (PerAF) has been added. (JIA Xi-Ze)</span></p> <p><span>&nbsp;</span></p> <p><span>Thanks a lot for your email to JIA Xi-Ze (</span><span></span><span>) for any suggestion.</span></p> <p><p><a href="" target="_blank">read more</a></p> Resting-state fMRI topics REST Sun, 24 Jan 2016 09:42:07 +0000 REST-Group 2345 at Dynamic brain connectome analysis toolbox <p><img align="left" alt="" src="" /><br /> 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.</p> <p><span>The&nbsp;latest&nbsp;release&nbsp;is&nbsp;</span><a href="">DynamicBC1.2_20160415</a><span>.</span><span>&nbsp;&nbsp;</span></p> <p><a href=";file=Manual%20DynamicBC1.1_20140710.pdf"><span>Manual</span><span>&nbsp;could&nbsp;also&nbsp;be&nbsp;downloaded</span></a><span><a href=";file=Manual%20DynamicBC1.1_20140710.pdf">&nbsp;here</a>.<br /> </span></p> <p>New features of DynamicBC 1.2 release 20160415:&nbsp;</p> <p>&nbsp;</p> <p>Fixed the step bugs when selecting window size.</p> <p>New features of DynamicBC 1.1 release 20140710:<br /> 1. Added the new utilties including the ‘Clustering’ and 'Spectrum' for dynamic FC/EC time series.<br /> 2. Added the new output of variance of dynamic FC/EC time series. &nbsp;<br />&nbsp;</p> <p>New features of DynamicBC 1.0 release 20140429:&nbsp;<br /> This release fixed some minor bugs in dynamic FCD.</p> <p></p><p><a href="" target="_blank">read more</a></p> Resting-state fMRI topics Tue, 08 Apr 2014 00:25:30 +0000 Wei Liao 1890 at