How can I extract only grey matter voxel signal?

Submitted by Eunji Jun on

I extracted 116 ROI region signal applied by AAL mask, but I need voxel-wise information.

I knew that functional information comes from grey matter, so I'm gonna extract all voxel signals in grey matter.

 

When I questioned same problem to you, you said to me that "If you want to process all the signals from every voxel, that means you have to know some programming skill. You can check y_Read.m."

so, to extract grey matter signal, in Matlab, I gave input 'wFiltered_4DVolume.nii' in FunImgARCFW directory to 'y_Read.m' and I thought that its output is grey matter signal.

But maybe it's not correct and I also did same process 'swFiltered_4DVolume.nii' in FunImgARCFWS directory to 'y_Read.m' and it's also not correct.

 

What does 'some programming skill'  means which you said to me before ? I've used matlab.

Please reply with more explanation.

Thank you!

 

YAN Chao-Gan

Wed, 10/05/2016 - 04:06

You can use y_Read, you get the time series of all the voxels. Then you apply a mask to get a region to get the signals of a given region.

You can read the code y_ExtractROISignal.m.

At Line 201:

SeedSeries_MultipleLabel(:,iElement) = mean(AllVolume(:,find(MaskROI==Element(iElement))),2);

You get the mean values of a given region.

Change it to

SeedSeries_MultipleLabel(:,iElement) = (AllVolume(:,find(MaskROI==Element(iElement))),2);

You get the signals of every voxel for that region.

'Some programming skill' means you can not understand what I said if you don't have it.