Hi Fabian,

The second image in your pdf looks fine as well, the yellow lines in there represent 0.25 apriori probability boundaries of a gray matter template (spm/TPM/TPM.nii) so the expectation is that most of your gray matter mask should like "within" those boundaries if it is correctly in MNI-space (which it appears to be). 

Regarding your file named "wc1cwc0csT1_RAS.nii", that indicates that your anatomical image has been normalized twice, which is not a good idea typically. Your gray-matter mask in MNI-space after proper preprocessing should be named "wc1csT1_RAS.nii", where the prefixes mean:

  w : normalized

  c1 : gray matter mask

  c : centered

  sT1_RAS.nii : your original structural image

representing a sequence of steps from right to left applied to your data (i.e. starting with your original structural image, that image was centered, and then it was normalized keeping the gray matter mask in MNI-space).

Instead, your file wc1cwc0csT1_RAS.nii prefixes mean: w (normalized) c1 (gray matter mask) c (centered) w (normalized) c0 (skull stripped) c (centered) sT1_RAS.nii (original structural image), which means that your data was normalized once, keepgin the skull stripped structural, and then that image was normalized again and this file represents the MNI-space gray matter mask output of that process.

Hope this helps

Alfonso

Originally posted by Fabian Wissing:

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!