[MINC-users] Clustering t-maps

[Paul GRAVEL]

Hi Jason,

Thank you very much for your help!

Just to clarify something though, would I set n to 50 to get clusters
of 50 adjacent voxels?

Best,

Paul

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
>