Dear SPMers,
I am new to VBM analyses using SPM8, and I am trying to make an
explicit mask during my statistical analyses. I’ve been having an
issue with gray matter regions outside of the glass brain when I look
at my results, and after looking at the forum it seems like the best
option might be for me to make an explicit mask. However, I am a bit
confused on how to make the explicit mask. I went to
http://www.cs.ucl.ac.uk/staff/g.ridgway/masking/ for information on
masking, and I am left with the following questions about using the
Batch GUI Mask creation:
Instructions say that “The standard approach is to make a mean image
and threshold it using the correlation-based optimality criterion”
1) I am assuming that the Optimal Thresholding method involve first
making an average (a separate option in the Batch GUI) and then using
this as the main image during the Optimal thresholding. Is this
correct?
2) Which input files do I put in to make the “mean image” mask? Do I
use the rc1*_.nii images to make a mask solely from gray matter, or do
I use the smoothed normalized images, or other files?
3) What is the “correlation-based optimality criterion”?
-I’m assuming that when I use the GUI, it’s the Corr(img,img<thr) option, yes?
Thank you for taking the time to read this, I just want to make sure
that I am doing this correctly since I have never made an explicit
mask before. I followed the Ashburner (2010) VBM tutorial, including
reorientation, new segment, creating DARTEL templates, and normalizing
to MNI space with a smoothing kernel of 10mm, and I input each
participant’s TIVs in the global calculation step.
Thanks for your help,
Jennifer Legault
Ph.D Candidate, Neuroscience
The Pennsylvania State University
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