How do I create a text file with a seed series?

Hello,

the question is in the subject. I would like to understand what exactly is a seed series and how do I create a text file with the seed series? I tried creating a text file with three columns (=coordinates), didn't work, four columns (coordinates plus radius) did not work either. I would like to calculate FC between the seeds I specify myself. Is it the right way to do it?

Any help is appreciated!

Thanks,

Lisa

Forums:

Hi Lisa,

DPARSFA->Define ROI->"Define Other ROIs"->Add Sphere

Then you put the X Y Z and Radius there, e.g.,

10 10 20 5
-10 10 20 5
6 10 20 5

Hey,

thanks a lot for your answer! Wouldn't it calculate the whole-brain voxel-wise FC for each of these spheres instead of calculating their FC with each other?

Thanks again!

 

Lisa

Hi Lisa,


If you check "Functional Connectivity", you will get the voxel-wise FC.

For ROI-wise FC, please see http://wiki.rfmri.org/content/extract-roi-time-courses-roi-wise-functional-connectivity

Hi Lisa,

Were you able to resolve this? I have the same issue and was unabel to resolve it after visiting the link recommended to you (Extract ROI Time Courses (ROI-wise Functional Connectivity)) and reviewing the training videos. I was recommended to use coeffcorr in MatLab, unfortunately I am a clinical psychology doctoral student and, as such, am not profficient in MatLab. Any suggestions would be greatly appreciated.

Thank you,

Felix

I assume you have extracted the ROI time series?

If so, you must have the correlation matrix.

If not, you can load the .mat file which contain the time series, and then type in:

R=corrcoef(ROISignals)

Hi Dr. Yan,

Actually the difficulty I had been having was with inputting the coordinates and radii using a text file ("+ Seed Series") for the purpose of extracing the ROI time series. I think my formatting was incorrect or perhaps it needed to be a *.mat file, because it worked once I entered the seeds individually (ie, "+ Sphere"). So far I was able to get the correlation matrices for 2 coordinates but I have quite a few more to estimate, can you please help me understand how to configure a file in order to use with "+ Seed Series"?

As a separate question: I have checked the box "Multiple Labels in mask file" because that is how I configured the atlas-based FC analyses (first with HOA, then aal), but is this still needed if I am defining spheres for "Extract ROI time courses"?

Many thanks in advance,

Felix

1. Please read http://rfmri.org/comment/4312#comment-4312 (my first reply) again. You don't need to use a txt file, just input all the coordinates in the Editbox.

2. No need in defining spheres.

Hi Dr. Yan,

1. Great, thank you. Yes, I was aware that coordinates can be entered individually through the Editbox, and now I see that for longer lists of coordinates (as with my analyses), it's possible to just copy-and-paste a series of coordinates directly into the Editbox.

2. That makes sense, thanks.

Best,

Felix