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

[Dylan WAGNER]

Hi all,

       On the minctotag issue:

	The more I think about it, the more it seems necessary for me to
have the true voxel values rather than rounded to the nearest integer.
Reason being is I'm correlating voxel intensities between two sessions in
the same subject. I'm hoping to generate a scatterplot of every voxel
in the first session against the same voxels in the 2nd session (both in
mni space).

	For whole brain, integers aren't so bad and with 900,000 voxel it
won't affect the shape of the distribution much. But once I do the same
for smaller ROIs I'm going to run into trouble if everything is integers.

        So! Anyone have any other methods? Since I'm correlating voxels I
need both coordinates and values. I presume it wouldn't be rocket science
to modify minctotag, however I honnestly would have no idea how to compile
it afterwards.

        Thanks,




> Hi Dylan,
>
> Hmmm... I took a look at the code, and minctotag rounds the voxel data
> values before writing them to the tag file.  I have no idea why, but that
> seems to be how the author defined the tag file format.
>
> It it becomes a nuisance it would be easy enough to fix, or to offer an
> alternative through mincextract.
>
> 	-bert
>
> On Tue, 16 Nov 2004, Dylan WAGNER wrote:
>
> >
> >
> >
> >   Hi Jason,
> >
> >        Thanks for the response. I wasn't aware of minctotag, and after
> > sniffing around, wow there's a lot more minc apps than on the wiki or bic
> > pages alone. I suppose that sounds a bit naive. I stumbled across a list
> >  at http://www.bic.mni.mcgill.ca/~stever/software_map.html
> > As I use some of these I'll try and add them to the wiki.
> >
> >    A few questions regarding minctotag.
> >
> >    So far it works great, however:
> >
> >       Voxel intensities are integers? The same minc in register gives me a
> > fair bit more precision. However for my purposes integers are fine, I'm
> > just curious why.
> >
> >
> >       Also thank you for the location of mincbet. So now I'm confronted
> > with three choices. Mincbet, skullstrip and the preprocessing method on
> > on the wiki page for VBM. It's a bloody buffet of skullstripping methods!
> > Any reason why one would be better? The method on the VBM seems more
> > tailored to each individual subject, though longer to carry out.
> >
> >              Best,
> >                    DDW
> >
> >
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
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