1. FreeSurfer does not fully segment the hippocampus on the surface.
2. I probably wouldn’t look at this in this way. In general, one wants the
brain to be roughly aligned well without major obvious deformations. If you
want an example of too much distortion, try ANTs.
3. The parcellation
Sorry, one more...we do have a command to put the coordinates of a surface
file into a metric file, so you can compute center of gravity in a
surface-based way. Use -surface-coordinates-to-metric, then either
-cifti-create-dense-from-template to put the coordinates into cifti,
followed by
Correction to the volume center of gravity part: if you convert to ROIs
before mapping to volume, you will have soft-edge "ROIs" in the volume, as
it accounts for partial voluming. You can use these as the weights in
-volume-weighted-stats (and you wouldn't need the -roi option) to take this
into
The command you are looking for is -metric-to-volume-mapping for an ROI, or
-label-to-volume-mapping for the entire label file. Note that these take
gifti inputs, so you will need -cifti-separate and possibly
-gifti-label-to-roi first (alternatively, -volume-label-to-roi
afterwards). We don't
It also occurs to me that if someone has already worked out even roughly
approximate locations for parcels (e.g., centers?) that correspond to volume
space coordinates in MNI-land, this would be "good enough" for me to finalize
the grant proposal in the next day or so. Admittedly, I'd rather
Another way to put this is that hippocampus is not cortical (it is part of the
medial wall), and thus FreeSurfer does not attempt to generate surfaces that
follow the structures in that region. They even have a FAQ on that specific
question:
Hello Aaron,
1. The hippocampus is a known area that FreeSurfer has a little difficulty with
so we don’t expect perfection in that area. The subject shown in the document
is quite good however.
2. Yes, "good" volume distortion has fewer blobs. The blobs are indicating
where the individual
