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FSL  August 2009

FSL August 2009

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Subject:

Re: TBSS clusters

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 28 Aug 2009 08:58:24 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (100 lines)

Hi,

On 27 Aug 2009, at 13:26, Mark Rees wrote:

> Hi,
>
> I have a large single, large cluster (1000+ voxels) present after TFCE
> correction at 0.001.  To explore this further I want to run some
> tractography from it.  As the cluster is so large tractography just  
> using
> this cluster is difficult to interpret, and selecting the COG or  
> voxel with
> peak p/t value within this cluster would lose a lot of information.
>
> In order to break down the cluster into smaller clusters and seed  
> from them
> I was wondering which of the following would be most valid or  
> whether they
> would give the same result:
>
> Approach 1:
> a) Take corrp image (image A) and apply clustertool using parameter  
> settings
> that break it down as much as possible (eg high threshold and low
> connectivity value)

I don't know what clustertool is?  However yes in general I would not  
change the connectivity in clustering for this purpose, just change  
the threshold, to allow you to find the most significant sub-parts of  
the large cluster.  You may find that there isn't enough value- 
resolution in the corrp image to allow this to be done very usefully,  
in which case you can instead re-run randomise, turning on the TFCE- 
enhanced tstat output option and setting the number of permutations to  
1. You can then apply the re-clustering to the TFCE-enhanced image.

> b) Mask zmax voxels in each cluster onto original corrp image (image  
> B) --
> ie left with an image of zmax voxels for each cluster

that's good too, or you could seed from the whole sub-clusters if you  
think they're small enough

> c) Deproject and backnormalise image B
> d) Create a small sphere aournd the voxels in image B and use as seeds
>
> Am I right in thinking this might not work as step c) may not result  
> in
> single voxels in native space for each cluster? (ie in deproject the  
> no of
> of voxels in the input does not equal the no in the output)

hopefully the latest versions should in general backwarp a single  
point to at least a single point - hopefully.

>
> Approach 2:
> As above but create sphere before deprojection and back  
> normalisation -
> might this have problems if the sphere lies off the group skeleton ?

Yes - that won't work, for that reason

>
> Approach 3:
> a) Take corrp image (image A) and deproject  into each subject
> b) Then apply clustertool with the same threshold and connectivity
> parameters to each subject
> c) Within each subject only accept clusters over certain size eg 10  
> voxels
> d) Within these clusters take zmax voxel and create sphere of set  
> radius
> around them
> e) Now backnormalise all clusters into native space and use as seed  
> in each
> subject

That's ok - but I think Approach 1 is probably best.

Cheers.



>
> Or perhaps someone might have a much better suggestion ?
>
> Thanks.
>
> Mark
>


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

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