[MINC-users] Clustering t-maps

[Paul GRAVEL]

Hi Jason,

Thanks again!  Now I understand!

Best,

Paul

On Wed, 23 Jan 2008, Jason Lerch wrote:

> 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
>  >>> _______________________________________________
>  >>> MINC-users at bic.mni.mcgill.ca
>  >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>  >>>
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>  >>
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