1) This script creates one new dset in the SUMA/ directory, called
fs_parc_wb_mask.nii.gz. This dset is a whole brain mask based on the
FS parcellation. Note that this is *different* than the
brainmask.nii* dset that FS creates. This mask is created in the
following way:
+ binarize aparc+aseg_REN_all.nii.*
+ inflate by 2 voxels (3dmask_tool)
+ infill holes (3dmask_tool)
+ erode by 2 voxels (3dmask_tool)
The final mask seems much more specific to the brain structure than
brainmask.nii*. It also removes several small gaps and holes in the
parcellation dset. In general, it seems like quite a useful whole
brain mask.
2) This script also makes three *.jpg files in the specified SUMA/
directory. The underlay in each is the *SurfVol.nii* dset. Each JPG
is row of axial, sagittal and coronal montages around the volumes
defined by the brainmask.nii*:
qc_00*.jpg : the overlay is the brainmask.nii* volume in red, and
the subset of that volume that was parcellated by FS
(in either the "2000" or "2009" atlases) is outlined
in black.
The idea for this formatting is that we do want to
see the official FS brainmask, but we might also
want to note its differences with the the binarized
aparc+aseg file. We might prefer using one or the
other dsets as a mask for other work.
qc_01*.jpg : the overlay is the fs_parc_wb_mask.nii.gz dset that
this script has created (see details just above).
qc_02*.jpg : the overlay is a set of tissues, like a segmentation
map of 4 classes:
red - GM - red
blue - WM
green - ventricles
violet - CSF+other+unknown
(from the *REN* files made by AFNI/SUMA).
qc_03*.jpg : the GM only
qc_04*.jpg : the WM only
qc_05*.jpg : the overlay is the "2000" atlas parcellation (from
the file: aparc+aseg*REN*all*)
