DPARSF ROI-wise connectivity

Submitted by MCube78 on Tue, 09/27/2011 - 22:32

Hi, I am trying to run FC on my data, and what I am interested in is ROI-wise correlations, rather than full brain values for each ROI. I see DPARSF generated one image per ROI (which I understand to be the correlation of each voxel with the timecourse of that ROI, as well as the z-transform of the correlation) Is there a way for DPARSF to output a matrix with the FC between all the ROIs I selected, or is the best way to do it to take the ROI_ROIFCMap.txt files for each ROI and correlate those? (these files are the preprocessed average timecourse for each ROI, correct?)

thank you

Martin

Forums:

ZHANG_RESTadmin

Tue, 10/04/2011 - 06:27

When you perform FC using DPARSF, you can see from the parameter setting window that there are two options: one is ROI-wise correlation, which does exactly what you want to do; and the other is voxel-wise correlation, which will produce an FC map for a ROI.

Hope it helps.
Han

MCube78

Tue, 10/04/2011 - 15:49

Hi Han,

thank you for the answer, but that is not quite what I see..
When I click on functional connectivity, and then click on the DEFINE ROI button all I see is a menu to input the ROIs, and in that I load in all my pre-defined masks. I don't see anywhere a button saying ROI-WISE or Voxel-wise. I did download the latest version though.

How do I find that button?

best

Martin

ZHANG_RESTadmin

Wed, 10/05/2011 - 06:54

Hi Martin,

You can try REST toolkit.
For detailed instructions please find the course on top of the website (Course menu).
In 'Data_Process_of_Rest_fMRI_Part1' you will see how to do.

MCube78

Wed, 10/05/2011 - 16:17

Thank you Han. Just to clarify, you are saying I cannot do ROI-wise FC with DPARSF but need to do it with REST?

I will give it a shot - thank you for the support!

Martin

PS: I should say that overall the suite is working very well with my data.. :)

ZHANG_RESTadmin

Sun, 10/09/2011 - 01:34

You're correct. Just check it in REST.
Hope it works well.

Cheers!
Han

MCube78

Mon, 10/10/2011 - 17:35

Han,

I just checked the "extract ROi timecourse" option and it worked like a charm (i.e., it writes exactly the ROI-wise correlation matrix I was looking for).

thank you!

martin

YAN Chao-Gan

Sun, 10/09/2011 - 15:10

Hi Martin!

You can find ROI-wise and Voxel-wise in REST.

For DPARSF, if you just check "Functional Connectivity", you can only get voxel-wixe FC map for each of your ROI.

However, if you want to get ROI-wise Functional Connectivity between your ROIs, you need to check "Extract ROI Time Courses" also. DPARSF will extract the ROI time courses for you and get the ROI-wise Functional Connectivity automatically for you. I think I have emphasized this part in the Video Course. I will update the English version of Video Course in soon since the English version is really ancient.