粉底液的用法
RESTing-state fMRI data analysis toolkit (REST) Manual
Xiaowei Song1, Xiangyu Long1, Y ufeng Zang1
1State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.
May 10, 2008
Thank Xiangyu Long very much for this English manual!
-- Xiaowei Song
Content
晒经石Some abbreviations (1)
1. What can you do by REST (1)
如何发财致富
2. Notice before using REST (2)
3. Start to u REST toolbox (3)
3.1 Installation (3)
3.2 Remove the REST (3)
3.3 Start REST (3)
3.4 Regional homogeneity analysis (4)
3.4.1 What is regional homogeneity analysis (4)
3.4.2.1 Remove linear trend (optional) (6)
3.4.2.2 Temporal filter (optional) (7)
3.4.2.3 Setting the input data (9)
3.4.2.4 Define the mask option (10)
3.4.2.5 Define the cluster size (11)
3.4.2.6 Configuring the output directory (11)
3.4.2.7 Calculating the ReHo map (13)
3.5 ALFF analysis (15)
3.5.1 What is the ALFF analysis (15)
蜗牛卡通图片3.5.2.1 Setting the ALFF parameters (17)
3.6 Functional connectivity analysis (19)
3.6.1Setting the parameters of functional connectivity analysis (20)
4. Websites (30)
5. Reference list (30)
6. Acknowledgement (33)
Some abbreviations
AAL: Anatomical Automatic Labeling template (Tzourio-Mazoyer et al., 2002)
ALFF: amplitude of low frequency fluctuation
AFNI: Free software, website: afni.v/afni
fMRI: functional magnetic resonance imaging
GUI: Graphical Ur Interface
MRIcron/Mricro : Free software, website:
婚礼场景
www.sph.sc.edu/comd/rorden/mricron/
ReHo: regional homogeneity analysis
REST: RESTing-state fMRI data analysis toolkit
ROI: region-of-interesting
SPM: Statistical parametric maps (Friston et al., 1995), a free software. 1. What can you do by REST
1.Batch processing of the fMRI data analysis;
2.Perform ReHo analysis, ALFF analysis and linear correlation
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analysis;
3.Band-pass filter, remove linear trend of the fMRI data
4.Viewing the time ries and power spectrum of the fMRI data
5.Define the ROI, extract the mean time ries within the ROI;
6.Viewing the MRI image, display the fMRI result on a anatomical
image;
7.Extract the specific cluster from the AAL template, Brodmann
template or statistic map, and create the mask image.
2. Notice before using REST
黄龙海拔1.Image file format must be ANALYZE 7.5, and MRIcron or AFNI
(Cox, 1996) can be ud to transform the format;
2.When processing the fMRI data by REST, fMRI data of each ssion
(or subject) must be stored in one folder volume by volume, i.e., each pair of files (hdr/img) is one time point. All volumes must be named in the order of the scanning quence, e.g., the fMRI data of one subject was stored in the independent folder, it means that there were exactly all volumes in this
folder and the files in this folder must like this: a001.hdr/img, a002.hdr/img, etc. Remember that, the unwanted image file must be moved out of the folder.
3.When using REST to define the ed voxel, if the coordinates of ed
was input manually, the original and the input coordinates of all images must be corrected, and the position of ROI can be viewed after clicking the “View ROI” button.
4.Cited this software as: RESTing-state fMRI data analysis toolkit
(REST, by Song Xiaowei, resting-fmri.sourceforge).
3. Start to u REST toolbox
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3.1 Installation
a)MA TLAB 2006b for Windows XP was recommended.
b)Unzip the package, then start MA TLAB, choo the option in toolbar
as following: File -> -> (Here lect the REST folder)->Save->Clo.
3.2 Remove the REST
Start MA TLAB, and choo the option in toolbar as following: File -> (Here lect the REST folder) -> Remove->Save->Clo, then delete the REST folder on the disk.
3.3 Start REST
1. Start MA TLAB.
2. Enter “rest” in the command line (Figure 1).
Figure 1, Enter …rest‟ to start REST toolbox GUI
3. After typing “rest”in the MA TLAB command line, the REST GUI interface will popup (Fig. 2).
Figure 2. REST main interface.
3.4 Regional homogeneity analysis
3.4.1 What is regional homogeneity analysis
Kendall coefficient of concordance (KCC) (Kendall and Gibbons, 1990) (Fig. 4) was ud for measuring the similarity of the time ries within a functional cluster bad on the regional homogeneity hypothesis (Zang et al., 2004). 27, 19 or 7 nearest neighboring voxels (Fig. 3) were defined as a cluster and a KCC value (range 0–1) was given to the voxel at the center of this cluster (Zang et al., 2004). Recently, this method was widely ud in the resting-state study (Cao et al., 2006; He et al., 2004,
