Questions With This Site

Wed, 12/03/2008 - 21:43 — dawnsong

Any questions you encountered with this site could be posted as a comment to this topic.
Please feel free to explore this researching site. I hope it be a start point of your resting-state fMRI research interest.

One advice is reading “How To Ask Questions The Smart Way”. And another advice may seem on the contrary: never hesitate to question yourself and then question in resting-state fMRI forum.

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Sat, 11/10/2012 - 17:54 — benileon

Re: Questions With This Site

Hi. I have a problem but it might be a Matlab problem. when I want to run slice viewer in rest it crashes in the moment of overlaying the reHo or the Alff results. When I Open REST I get the following message:

Warning: image_toolbox not valid
> In rest_sliceviewer>InitControls at 1053
In rest_sliceviewer at 74
In rest_sliceviewer at 38
In rest at 153

I have added the Image_processing_Toolbox81_win64 to the patth but still not working. Any ideas?

Thanks!

Fri, 11/16/2012 - 00:46 — yanrui15

Re: Questions With This Site

Frist I feel so sorry that I did not response you timely .I suggest that you can try to use SPM to see whether the problem still exists.I think it may be better to consult the software R & D by Professor Yan Chaogang who will give you informed answers

Fri, 11/16/2012 - 23:58 — YAN Chao-Gan

Re: Questions With This Site

I think his problem is the installation of imaging processing toolbox for MATLAB.
BTW, I am not a professor yet. :)

Tue, 11/13/2012 - 00:21 — YAN Chao-Gan

Re: Questions With This Site

Hi,

Seems the image processing toolbox is not working. Or please re-install it by providing a license?

Tue, 09/18/2012 - 23:24 — 求索脑功能

多组数据处理的ICA分析

各位老师好，我采集了一些静息态数据，现在把这些数据配对分成了六组（3对），想用独立成份分析（GIFT）看他们的成分差异，能不能一次把六组的数据都处理了？因为如果分成六次处理，然后挑选成份统计分析的话，我觉得应该会主观误差太大了，而且可能会遗漏成份，有没有让他们成份对应，然后可以方便区分成份的方法。谢谢

Wed, 09/19/2012 - 00:40 — ZHANG_RESTadmin

可以而且应该一次把六组处理了。

Wed, 09/19/2012 - 20:57 — 求索脑功能

如何设置被试呢？

谢谢老师！可是我六组的数据并不一样多？分成三对后，数目各不相同。这样在用GIFT处理的时候，我就不知道该怎么设置了，试着分成两组三个session的话也会报错。这样应该怎么设置？请老师指导下具体的设置。谢谢！再次感谢老师的回复！

Wed, 09/19/2012 - 21:18 — ZHANG_RESTadmin

可以把6组看成不同的被试，不用session的那个，就是不

可以把6组看成不同的被试，不用session的那个，就是不同的被试。结果做出来后你在一一分开即可。

Sun, 01/13/2013 - 21:22 — fish

Re: 可以把6组看成不同的被试，不用session的那个，就是不

我想问老师一一分开具体是怎么做的呀？因为gift是以sub为单位打包压缩的，是把他们解压缩后，找到想要的component后，再做成文件夹吗?我用spm做one-sample t-test，用全脑做mask，没有发现任何voxel，到底是为什么呢？

Sun, 09/16/2012 - 21:57 — 求索脑功能

AlphaSim和FDR校正严格性谁更大？

各位老师：
做静息态数据统计分析的时候，是不是模板应该选择的尽量的小，这样在做AlphaSim的时候就能用更小的cluster size值做阈值？为什么我的结果用FDR校正的时候有阳性结果，而用AlphaSim校正后就基本没有结果了。是不是先验知识不足的情况下，AlphaSim校正更严格？如果我用一个比AlphaSim小的阈值做出了结果，能报出来吗？应该怎么报？
谢谢！
致敬！

Mon, 09/17/2012 - 01:29 — yanrui15

AlphaSim和FDR校正

你好，我也对你提出的问题感兴趣，AlphaSim和FDR校正的原理不是一样的，所以结果用FDR校正的时候有阳性结果，而用AlphaSim校正后就基本没有结果了。FDR矫正在体素多的时候更严格，用一个比AlphaSim小的阈值做出了结果，只能说明他禁不起AlphaSim矫正，可能经不起噪音等的影响，结果的可靠性是存在疑问的，但是也不代表他没有意义。

Tue, 09/18/2012 - 02:45 — YAN Chao-Gan

Re

通常意义上的FDR校正是不考虑空间宽度的，而AlphaSim和Gaussian random field theory correction是需要考虑空间宽度的。
你看一下FDR校正之后的结果零散吗？

Tue, 09/18/2012 - 21:05 — 求索脑功能

致谢，追问

谢谢严老师回复。FDR得到的结果并不零散，是不是如果结果包含的体素较少时，使用FDR比AlphaSAim能保留更多的激活区，另外，如果我校正时使用的cluster阈值比AlphaSim要求的阈值下，报告结果的时候应该说校正了吗？

Wed, 09/19/2012 - 00:45 — YAN Chao-Gan

Re

如果不零散，应该不会经不起AlphaSim校正呀。
cluster阈值比AlphaSim要求的阈值下？？

Wed, 09/19/2012 - 20:51 — 求索脑功能

是的

谢谢严老师。是的，因为我用的半高全宽比较大，需要的阈值比较大，得到的cluster比AlphaSim要求的要小。如果我使用比AlphaSim小的阈值，感觉结果还是挺好的，也能一定程度上解释。不知道这样行不行？报告的时候说校正的了吗？再次感谢严老师！

Thu, 09/20/2012 - 01:27 — YAN Chao-Gan

Re

你用FDR校正，也是可以接受的。

Mon, 04/02/2012 - 21:11 — yanrui15

请高人指点如何查看rest slice view的结果？

小弟我试着做了统计，用rest slice view得出结果，但是看不懂结果，请高人指点下，非常感谢
# voxels structure（对于voxel structure，这个是否指16个相接的体素每个体素的部位？下表中如此分散，例如：左侧海马只有2个voxel BA34区就一个voxel，这些点有没有意义？）
16 --TOTAL # VOXELS--
3 Midbrain
3 Left Brainstem
2 Limbic Lobe
2 Hippocampus_L (aal)海马
2 ParaHippocampal_L (aal)左侧海马旁回前扣带回皮层
2 Parahippocampa Gyrus
2 Left Cerebrum
1 brodmann area 34前扣带回皮层
1 Gray Matter
----------------------
Cluster 4
Number of voxels: 32
Peak MNI coordinate: 45 48 -15
Peak MNI coordinate region: // undefined // undefined // undefined // undefined // undefined // Frontal_Mid_Orb_R (aal)
Peak intensity: 3.9619（例如这个peak点在右侧额中回眶面，而右额中回有18个体素，右额中回眶面、额下回眶面分别有16个# voxels structure 和 15个体素，在报告结果时是否需要都报出来，还是只报右侧额中回眶面？其他脑区如BA11区怎么办？）
32 --TOTAL # VOXELS--
24 Right Cerebrum
21 Frontal Lobe
18 Middle Frontal Gyrus
16 Frontal_Mid_Orb_R (aal)右侧额中回眶面
15 Frontal_Inf_Orb_R (aal)右侧额下回眶面
6 brodmann area 11 额眶区（眶回，直回和上额回前侧的一部分）
6 Gray Matter
5 White Matter

Sat, 07/28/2012 - 13:17 — Wini

Voxel masking

Hello, I have some Resting state fMRI data an I want mask the voxels and use aal.but I dont know how to do?

Wed, 08/08/2012 - 09:16 — yanrui15

你好，我英语太差，如果用中文的话，我非常乐意和你交流下fMRI。

Thu, 01/12/2012 - 16:27 — legend_long

有关AAL模板问题

如果我要知道AAL模板中某个具体区域（比如Thalamus）所有点的坐标，应该如何获得？

Tue, 11/29/2011 - 13:35 — WHJUNG

Parametric test with GCA output

Dear REST experts,

Thanks for your recent works, REST-GCA :)
I am trying to perform granger causality analysis using REST-GCA. I conducted both coefficient-based and residual-based GCA for controls group and patients group and got several outputs for each group. These outputs were finally transformed into Z-value. Now, I'd like to perform between-group comparison using parametric test (i.e., two sample t-test). However, I am not sure what output files I use to do this.
(1) Is it right that two outputs ("GCA_x2y_1" and "GCA_y2x_1", which are not z-transformed values) for coefficient-based GCA are used to perform between-group comparison?
(2) Is it right that four outputs ("GCA_x2y_Transformed", "GCA_y2x_Transformed", "ZGCA_x2y_Transformed", and "ZGCA_y2x_Transformed") for residual-based GCA are used to compare both groups?

Please comments.
Thank you in advance.

Sun, 11/27/2011 - 17:40 — yzgwj

请问一下用Dparsf选了DICOM to Nifiti以后，出现这个错误，是不是与原数据文件有关呢？

我用的是matlab2009a的版本，原数据是用西门子设备采集的，它的文件是没有扩展名的
??? Undefined function or method 'spm' for input arguments of type 'char'.

Error in ==> DPARSF_run at 120
[SPMversion,c]=spm('Ver');

Error in ==> DPARSF>pushbuttonRun_Callback at 939
[Error]=DPARSF_run(handles.Cfg);

Error in ==> gui_mainfcn at 96
feval(varargin{:});

Error in ==> DPARSF at 41
gui_mainfcn(gui_State, varargin{:});

??? Error while evaluating uicontrol Callback
谢谢！

Tue, 11/29/2011 - 00:23 — YAN Chao-Gan

Thu, 12/11/2008 - 13:47 — dawnsong

Cool Cumulus Cloudy Tags support!

I added cumulus tags to this site. It spent me 1 days or so. But one look at the effect make me proud of it. It deserved.

I hope it would help you too.

Wed, 12/10/2008 - 14:41 — dawnsong

Double Click left menu to show its content

Double Click the menu on the Left of this site to show its content.
Single Click the menu will show its submenu when there is any submenu item.

dawnsong

Tue, 12/09/2008 - 21:24 — dawnsong