ZangYF Group's CVs

Out of memory--Error message for running ReHo and FC tools

Submitted by Haibo on Tue, 04/14/2009 - 09:04
Dear REST experters:

      I am new to run REST toolbox. When running ReHO and FC, get the following error messages. I don't know what wrong I did. BTW, do you have some stand along program or easy tools for extracting the time course data. Thanks in advance.

Haibo

error messages:

Forums: 
Resting-state fMRI topics

关于去除头动的影响的一个小问题

Submitted by zqbaxfgg on Mon, 04/20/2009 - 15:59

我想请问一下rest中fc.m关于去除头动干扰的源码程序
if ACovariablesDef.polort>=0,
thePolOrt =(1:sampleLength)';
thePolOrt =repmat(thePolOrt, [1, (1+ACovariablesDef.polort)]);
for x=1:(ACovariablesDef.polort+1),
thePolOrt(:, x) =thePolOrt(:, x).^(x-1) ;
end
end
% switch ACovariablesDef.polort,
% case 0,
% thePolOrt =ones(sampleLength, 1);
% case 1,

Forums: 
Resting-state fMRI topics

RE: long mixed session of rest and task

Submitted by ZangYF on Thu, 04/23/2009 - 06:44

A long session, 22 minutes: Resting state 9 minutes, and then a blocked design (2 minutes task + 30s rest) 13 minutes. The questions are:
(1) Is the head motion a concern?
(2) Can the 9-minutes rest be used as a baseline for the data analysis of the blocked design?

My answer:
(1) Yes. There may be more head motion for such a long session. But occasionally, a long rest is necessary (e.g., epilepsy and sleep study).

Forums: 
Resting-state fMRI topics

ReHo: quickly get the ranks for matrix

Submitted by restbrain on Fri, 04/24/2009 - 13:59

Hi, Xiao-Wei

I just write these here and suggest you use methods below to get the ranks more quickly:
(here I suppose symbol V means a 4D fMRI matrix)
%-----------------------------------------------
[Y,I]=sort(V,4);
[X,R]=sort(I,4);
%-----------------------------------------------
R should be the ranks 4D matrix, which can be used for ReHo computation. These two lines code make computation faster in MATLAB (around 10s for one 4D fMRI data).

Say hi to your guys
XINIAN

Forums: 
Other

静息态研究

Submitted by sunshine on Fri, 05/01/2009 - 14:27

各位老师：
      大家好！我记得曾经看过一篇文章上说静息态默认网络中的脑区在有刺激的作用下时信号会降低，但现在一直没找到当时看的那篇文章，想请问各位老师是不是真有这个结论，如果有含有这个结论的文章能否给我传一份？谢谢！我的邮箱是：qiuwenjuan1014@yahoo.cn

Forums: 
Resting-state fMRI topics

Q&A: "REST error...ReadNiftiImage.m"

Submitted by YAN Chao-Gan on Wed, 05/06/2009 - 09:44

Hello,

I am trying to analyze some resting state data using REST, but I cannot load the data in the GUI.  Am I correct to assume we need to enter data in conseqcutive file names of ANALYZE format?  The error message I get in Matlab refers to line 103 of rest_ReadNiftiImage.m

Is this script necessary if we are using ANALYZE not NIFTI?  If it is not necessary how do I skip it.

I do not know how to proceed.  Any assistance would be greatly appreciated.

Thank you,

Carlos

Forums: 
Resting-state fMRI topics

REST functional connectivity error 'Matirix dimensions'

Submitted by YukiSakai on Sat, 05/16/2009 - 00:58

Hi, REST exparts

 I'm trying to analyze my resting state fMRI data using by REST functional connectivity. I've tried many times, but I always encount this error.

Exception occured
Error using ==>eq
Matrix dimensions must agree

I think that dimensions of my data don't match. Dimensions of my data are 79X95X69(Vox size 2X2X2, smooth 6mm). How can I solve this probrem? I'm sorry I'm just a biginner.

 Thanks in advance.
Sincerely,
 Yuki

Forums: 
Resting-state fMRI topics

Pleae resmaple your mask or ROI definition file first!

Submitted by YAN Chao-Gan on Mon, 05/18/2009 - 13:39

Hi, Cleofé Peña Gómez!
     1. You need to resample your mask or ROI file to the dimension of your functional images.
          There were three ways: (1) use SONG Xiao-Wei's program, from http://restfmri.net/forum/node/78                              

                                                 (2) use my program, from http://restfmri.net/forum/node/81   (the third one)
                                                 (3) use SPM5:
                                                                       a. Click "Coregister"
                                                                       b. Click "New "Coreg: Reslice""
                                                                       c. "Image Defining Space": choose one of your functional image. e.g. your normalized functional image or image after Detrend and Filter.
                                                                       d. "Images to Reslice": choose the mask file or ROI definition file. e.g. BrainMask_05_61x73x61.img
                                                                       e. "Reslice Options" -> "Interpolation": choose "Nearest neighbour"
                                                                       f. Just click "Run". Then you will get the resmapled mask or ROI file with a surfix of "r".
      
Forums: 
Resting-state fMRI topics
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