[MINC-users] Clustering t-maps

[Jason Lerch]

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
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