Dear all,
I just found that the equivalence Volume/integral isn't quite correct. The equivalence must be between the volume and something like an expected value of the histogram V = E[H] = ∫xH(x)*dx* (where x is the greyscale value).
So, the point 2) described in my previous email becomes (with some intermediate passages)
Find the threshold value *thr* such that:
Does this make any sense to you?
Luigi.
2014-09-08 9:49 GMT+02:00 Luigi Antelmi luigi.antelmi@gmail.com:
Dear list members,
as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages) that operates by summing up all the greyscale values https://github.com/neurodebian/freesurfer/blob/master/GEMS/kvlQuantifyPosteriorProbabilityImages.cxx#L107 (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map.
What procedure do you use or suggest?
I think there are two possibilities here.
- As written in the paper from Van Leeput et al.
http://www.ncbi.nlm.nih.gov/pubmed/19405131, I can *"assign each voxel to the label with the highest posterior probability"*. Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones.
- Threshold the subfields such that the volumes of the thresholded mask
will equal those calculated by integrating the histogram on the domain 0-255; Formally, find *t* such that:
where *H* is the histogram of the subfield.
I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling.
What do you think about?
Luigi.
