Hi there,

I have some questions regarding the slice viewer.

1. White matter ROI:
   
   
   
   • ROI tools → Display slice viewer with structural overlay (QA_REG): looks well aligned (please see attached screenshot).
   
   
   • ROI tools → Display slice viewer with MNI boundaries (QA_NORM): does not look well aligned (please see attached screenshot).
   
   
   • Why is that, if the file is supposed to be in MNI space? When I load the file Wc1cwc0csT1_RAS.nii in FSLeyes, it is in MNI space.
     → Is the file in MNI space or in subject space?
     → What do the letters in the filename (Wc1cwc0csT1_RAS) stand for?
   
   
   
   
   
2. Grey matter ROI:
   

ROI tools → Display slice viewer with structural overlay (QA_REG): please see attached screenshot

1. 
   
   
   
   1. What does CONN use for the brain image and the yellow outline?
      Is the background brain the subject’s anatomical image in MNI space, or something transformed?
      Tooltip says: “Slice viewer with func/struc overlay displays ROI contours overlaid with mean functional or same-subject anatomical volume.”
      → What exactly does functional mean here?
      
   
   
   

3. Functional data:

func tab → Display slice viewer with anatomical overlay (QA_REG): please see attached screenshot

• 
  
  
  
  • Are the fMRI brains already in MNI space?
    Tooltip says: “slice viewer with anatomical overlay displays mean functional overlaid with same-subject structural volume.”
  
  
  
  

Thanks in advance!