FC of 2 seeds

Submitted by merrf on Mon, 01/09/2012 - 21:28

Dear REST authors,

I'm trying to analyze seed-based functional connectivity of the thalamus by using REST and DPARSF.
Here's my simple query: How can I perform FC of the two seeds at the same time (e.g., intrinsic connectivity of both left and right lateral thalamus simutaneously, intead of right and left thalamus, respectively)?

Thank you in advance for your kindness.

Best Wishes
Kim
Seoul, South Korea

Submitted by YAN Chao-Gan on Tue, 01/10/2012 - 02:34

Just let your ROI mask file include both the left lateral thalamus and right lateral thalamus.

If you have two ROI files, REST->Utilities->Image Calculator: (i1+i2)~=0

Submitted by merrf on Tue, 01/10/2012 - 21:33

Dear Dr. YAN Chao-Gan

Thanks for the quick response.
What you have mentioned seems clear to me.

In the mean while, I want to use 'Define ROI' and successive 'spherical ROI' functions of DPARSF GUI (i.e., MNI coords of both thalamic nuclei and radius of 3 mm).
Is it possible to perform FC analysis of these 2 spherical ROIs simutaneously?

Thank you in advance for your kindness.

Kim

Submitted by YAN Chao-Gan on Thu, 01/12/2012 - 06:14

Use the following scripts to do that:

RefFile='/Data/FunImgARW/Sub_001/xxx001.img'; %Specify one of your functional image
OutputMaskFileName='TwoROIInONeMask.img'; %The output file name
ROICenter=[-20 30 30;20 30 30]; %The ROI Center
ROIRadius=6; % The ROI Radius

ROIDef=[];
for i=1:size(ROICenter,1)
ROIDef=[ROIDef;{rest_SphereROI('ROIBall2Str', ROICenter(i,:), ROIRadius)}];
end
[RefData,RefVox,RefHeader]=rest_readfile(RefFile);
MaskSum=0;
for iROI=1:length(ROIDef)
MaskTemp=rest_SphereROI( 'BallDefinition2Mask' , ROIDef{iROI}, size(RefData), RefVox, RefHeader);
MaskSum=MaskSum+MaskTemp;
end
rest_WriteNiftiImage(MaskSum~=0,RefHeader,OutputMaskFileName);

Submitted by merrf on Thu, 01/12/2012 - 22:31

Dear Dr. YAN Chao-Gan

Thank you for your kindness.

According to your explanation, it seems that method for 2 seeds analysis by using GUI is not possible, right?
The script you wrote seems hard for me to perform, because I'm not familar with matlab language.
However, I'll try what you have indicated.

Kim