I have some queries about FIRST. BTW this seems to be a great tool, which
makes it very practical to analyze subcortical volume/shape, but could also
be very useful for providing individual anatomical ROIs for functional
I have been using this for an exploratory investigation hippocampal
volume/shape in some subjects from a VBM (SPM) study I have already run.
I followed the instructions on the first webpage
("http://www.fmrib.ox.ac.uk/fsl/first/index.html"), and was able to segment
the hippocampus and subcortical structures. I then used first-utils to run a
vertex analysis on the results, again following the instructions closely,
except mine is a correlation design (rather than group comparison). I was
able to view the results in FSL-view, where they corresponded well with what
I would have expected from the VBM analysis. I think they add to the VBM
results, and I'd like to include them in any publication, but before that
I'd like to read a more detailed description of the vertex analysis (as
opposed to the segmentation).
Here are some concrete questions:
i) For each vertex, what exactly is being fitted to the regressors in the
ii) Results: I'd also like to know (daft question) what the units are in the
vtk-files that are produced as output (Z-scores?) and displayed in FSL, and
more generally what is the format of the output files. It might also be
useful to know the bvars file format.
I found it difficult to control the visualisation in FSL-view. So far as I
can see, it is hard to include more than one mesh (you can add them, but you
cannot select them individually to vary e.g., the range of the colour bar).
For example, I'd like to have more control over the colourmap used, and I'd
like a more constrained view (e.g., axial, orthographic projection avoiding
perspective artefacts) and to include both one hippocampus. For these
reasons I'd prefer to import the data into e.g., matlab, blender in order to
produce better figures. The format of the vtk files seems very readable, but
to avoid mistakes it would be useful to get an authoritative description of
the file format.
I understand that two meshes are produced (one representing the mean shape
of subjects where the covariate is less than the mean, one the mean for
those for whom it is greater - one can morph between the two using the mesh
slider. However, this doesn't capture the full range of variation in the
data, and it might also be interesting to see the vertex-wise results
projected on the more extreme meshes or, perhaps, on a "standard" mesh.