[MINC-users] Mincextract to get voxel values and coordinates?

[Peter Neelin]

On Mon, 15 Nov 2004 21:35:59 -0500, Dylan WAGNER
<dwagne@bic.mni.mcgill.ca> wrote:
> 
>    I'm trying to get a table of voxel values and coordinates above a
> certain threshold. Which tool would be most appropriate for this?
> 
> find_peaks with the distance set to 0 still doesn't give me every single
> voxel (I know this because mincstats tells me I have 11,000 voxels above
> threshold and find_pos only gives me about 90).

find_peaks was designed to do exactly this task. mincstats is telling
you how many voxels are above the threshold. find_peaks tells you how
many peaks are above threshold (a peak is a voxel that is greater than
all of its neighbours). Most voxels above threshold are not
interesting - they are on the side of the mountain, so to speak.
Generally, one is only interested in the peaks, unless you want to
evaluate something like the area of the peak. If your input data is
fairly smooth, then having only 90 peaks above threshold is not
surprising. Having 11000 voxels above threshold tells you something
about the area above threshold, not the peaks.

The only weirdness that I can recall in the output of find_peaks is
the handling of plateaus (a flat peak). I think that all of the edge
voxels are identified as peaks. You should not usually see this type
of structure in fMRI or PET data, however. Note also that by default
find_peaks suppresses edge peaks, since these are generally not true
peaks, but artifacts of the volume boundary. You can change this
behaviour with the -include_edges flag.

You can persuade yourself that find_peaks is in fact working by
loading the tag file into register with the original volume (I cannot
remember if you have to give two volumes). Set the lookup table
minimum to your threshold and then step through the list of peaks
(with the down arrow), or simply stack through the volume. You should
see that all visible peaks have a corresponding circle (identifying a
tag).

The intensity value of the volume at the peak is given as the label of
the tag (the string at the end of each tag line).

Peter