[MINC-users] minimum cluster size

[Jonathan DuBois]

Thanks Andrew, that worked well. 

On 2012-05-31, at 12:00 PM, minc-users-request at bic.mni.mcgill.ca wrote:

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>   1. minimum cluster size (Jonathan DuBois)
>   2. Re: minimum cluster size (Andrew Janke)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 30 May 2012 13:45:11 -0400
> From: Jonathan DuBois <jonathan.m.dubois at gmail.com>
> To: minc-users at bic.mni.mcgill.ca
> Subject: [MINC-users] minimum cluster size
> Message-ID: <3C622EE4-0E80-4086-A24F-C6D740C6878E at gmail.com>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Minc Users, 
> 
> Does anyone have a script or method for setting a minimum cluster size for a minc image? I would like to only view significant voxels (greater than a specified p-value) in a cluster of 3 or more for a z or t map. Thanks in advance. 
> 
> Jon
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 31 May 2012 12:23:39 +1000
> From: Andrew Janke <a.janke at gmail.com>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] minimum cluster size
> Message-ID:
> 	<CAG0CB22PA3kQgBvLaiX0iucfVd7J_Skza+QD7kW25zzkVj9fuA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Jonathan,
> 
> On 31 May 2012 03:45, Jonathan DuBois <jonathan.m.dubois at gmail.com> wrote:
>> Does anyone have a script or method for setting a minimum cluster size for a minc image? I would like to only view significant voxels (greater than a specified p-value) in a cluster of 3 or more for a z or t map.
> 
> I don't know of a specific tool for this but here's what I'd do:
> 
> # find all voxels above your threshold
> mincmath -gt -const <thresh> tmap.mnc thresh.mnc
> 
> # use mincmorph to find the groups (using a 3D 6 connectivity kernel)
> # mincmorph will order the groups by size.
> mincmorph -group -3D06 thresh.mnc groups.mnc
> 
> # use mincstats to find the number of values in each group via a histogram
> mincstats -histogram hist.txt -discrete_histogram group.mnc
> 
> Then look at hist.txt and find the group number that suits the number
> of voxels you want in each group. You can then find all groups greater
> than this by a simple threshold
> 
> mincmath -gt -const <group-threshold> group.mnc mask.mnc
> 
>> From there you can just apply the final mask to your original data
> 
> mincmath -mult tmap.mnc mask.mnc tmap-masked.mnc
> 
> 
> 
> a
> 
> 
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> End of MINC-users Digest, Vol 82, Issue 2
> *****************************************