Resting-state fMRI topics

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)

Submitted by YAN Chao-Gan on Fri, 05/06/2011 - 19:07

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: 
REST
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Resting-state fMRI topics

关于alphasim校正的问题

Submitted by liufeng on Mon, 05/02/2011 - 20:42

我想问的问题是我用alphasim校正，用了三组。首先p=0.005算出cluster size是406，用p=0.001算出cluster size是183，用p=0.01算出cluster是624；我选的cluster size都是第一个alpha小于0.05所对应的size。那么他们的结果都是产生了一个p=0.05的校正吧？如果是，我分别用三组校正去看我的spmt0001.img，校正后的结果不一样。

p=0.001cluster size183这一组最强，校正后没有任何结果，p=0.01cluster624这一组校正最弱，出来很多结果。我想问一下如果都是模拟的p=0.05，那么出来的结果为什么不一样呢。

期待您的回复！

Forums: 
Resting-state fMRI topics

Rest 2 sample T test error

Submitted by yhcha@mednet.uc... on Sun, 05/01/2011 - 12:25

Hi everyone, With great help from this forum, I was able to get the first level analsysis done through DPARSF. I am trying to do a two sample T test with 5 patients and 5 controls. I add an age text file as the covariate. I get this error message below.
Thanks for your help in getting past this hurdle.
Yoon-Hee

Forums: 
Resting-state fMRI topics

how to explain the "search volume" in spm?

Submitted by xuercan on Wed, 04/27/2011 - 06:58

最近，被review问及了一个问题，如下：
It was unclear to me the nature of the correction cited for the correlation of CESD(抑郁量表) with ICA signal. Was this voxelwise or clusterwise? What was the search volume?

关于第二问我很费解，What was the search volume. 这个要我回答什么呢？ 关于search volume，见附件。如何正确的回答他这个问题，search volume 的官方解释到底是什么，我查了很久，没找到书面的解释。请高人多多指点。

Forums: 
Resting-state fMRI topics