[MINC-users] Clustering t-maps

[Paul GRAVEL]

Hi Marc,

Thank you; it works like a charm!

Best,

Paul

On Wed, 23 Jan 2008, Marc BOUFFARD wrote:

> Another way to get the same output as with mincmorph step below is with a
> matlab program called locmax.m which is part of the fmristats package.
>
> On Wed, 23 Jan 2008, Jason Lerch wrote:
>
> > Hi Paul,
> >
> > mincmorph is your friend. The algorithm is something along the lines of:
> >
> > mincmorph -successive 'B[4.0:999]G' input_t_map.mnc output_clusters.mnc
> >
> > This will give you a map of connected blobs of voxels all above a
> > t-value of 4.0 (change that to reflect the threshold you want), numbered
> > according to size of the connected blob (i.e. 1 is the largest blob, 2
> > the second largest, etc.) Then use
> >
> > mincstats -volume -binvalue n output_clusters.mnc
> >
> > to find the smallest n (which should be an integer) still above the size
> > that you want for your clusters.
> >
> > mincmath -seg -const2 0.5 n.5 output_clusters.mnc clusters.mnc
> >
> > with that n determined by mincstats will then give you a map of all the
> > voxels that are part of a cluster of the size that you would like to have.
> >
> > Hope this helps,
> >
> > Jason
> >
> > Paul GRAVEL wrote:
> > > Dear All,
> > >
> > > I currently have some t-maps, calculated using matlab, in minc format.
> > > >From this t-map.mnc file I would like to create another minc file, but
> > > with only clusters, say of 50 adjacent voxels with a t > 4.  Would anyone
> > > have a script, routine or algorithm to perform this operation?
> > >
> > > Any help would be greatly appreciated!
> > >
> > > Best,
> > >
> > > Paul
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>