Hi, Austin-
Please note the full description of the [4]th volume:
[4] = binary mask for gray matter plus some CSF (slightly dilated)
++ this volume is not used in this script
++ it is intended for use in restricting FMRI analyses
to the 'interesting' parts of the brain
++ this mask should be resampled to your EPI spatial
resolution (see program 3dfractionize), and then
combined with a mask from your experiment reflecting
your EPI brain coverage (see program 3dmask_tool).
... namely that it is an *inflated* GM map, that includes more than just the GM of the template itself (many templates come with tissue maps, too).
The idea of inflating it is to provide a mask that cover GM of perfectly aligned data *and* GM of non-perfectly aligned data. While SSwarper and the 3dQwarp alignment tools underneath are quite good, they are not perfect; and there is *a lot* of variability across human brains to try to overcome, like different numbers of sulci/gyri in a given part of the brain across a group.
So, how much this expanded GM is useful for your analysis depends on what specifically you want to do. What do you want to do with this GM mask?
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On separate AFNI notes of selecting/resampling volumes like this:
If you wanted to make a separate volume of *just* that [4]th volume of the MNI-SSwarper reference dset, you could do something like:
3dcalc -a MNI152_2009_template_SSW.nii.gz"[4]" -expr "a" -prefix MNI152_2009_template_SSW_vol4_only.nii.gz
If you had some output EPI data in the MNI space at a particular resolution, you could both grab the [4]th volume and resample it to that grid with:
3dresample \
-input MNI152_2009_template_SSW.nii.gz"[4]" \
-master DSET_EPI_IN_MNI \
-rmode NN \
-prefix MNI152_2009_template_SSW_vol4_only_res2epi.nii.gz
--pt
