[MINC-users] Clustering t-maps

[Jason Lerch]

Paul GRAVEL wrote:
 > 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?
No - the clusters are ordered in size of the cluster, and there is no 
way of knowing what size each cluster will be beforehand. That's what 
that mincstats command was for - use that to find the cluster volume 
that you need for your threshold. It might be cluster 50, or cluster 10, 
or 100, etc.

Cheers,

Jason

 >
 > 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
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 >>>
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