Question: how to create ROI mask for functional connectivity?

Submitted by Grace on Tue, 10/14/2014 - 05:12

Hi,

I am Grace. I am a beginner of the resting-fMRI analysis.
I want to use a user-defined ROI for a functional connectivity analysis.

I am wondering if you could tell me how to create ROI images with the MNI template using the REST gui step-by-step. 
For instance, if I am interested in functional connectivity between the dorsolateral prefrontal cortex and the ACC,
how could I create the ROI images for those regions?

Thank you so much in advance,

Grace

Submitted by Grace on Wed, 10/15/2014 - 01:36

I found the old posts in regard to ROI mask files stating as below. Still, I have a couple of questions. I got the AAL template from the MRIcroN and resampled the AAL template using SPM. Then, I went to the sliceviewer in REST and entered specific coordinates, X, Y, Z in which I am interested in the sliceviewer to create a ROI file. Then, I am not sure what to do next. I also could not find "Save2Mask" in the slice viewer. Where can I find it? Also, if I should take more steps to make a ROI mask image, please let me know! Thank you! - Grace

***General steps to create ROI mask***

1. Resample the AAL or BA template (available in MRIcroN) if the template is not the resolution of your functional data according to http://www.restfmri.net/forum/Course.
2. Make the ROI file. Use rest_sliceviewer to open the resampled template, and click on a region you wanted, then use "Save2Mask" button to save the region in a ROI file.
3. Use REST to do the FC analysis. I think you have known the steps already.
Further, if you want to extract the AAL time courses, you also can try DPARSF.



***How to resample a ROI file***

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".
      

2. This warning does not matter. By the way, The latest release is  REST V1.3 Reslese 090422, please download it from restfmri.net. And you can post your further questions there.
       Best wishes!
                                                                                YAN Chao-Gan