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Hi Bonnie,

When the threshold is specified, a mask of the surviving clusters is created, and this mask is fed into atlasquery. If the clusters are large (here the #1 has 49015 voxels), the probabilities for the structures get "diluted" when averaged for all the voxels in the mask, and you see small values for the percentages. You probably saw already the documentation of atlasquery, and here it's the same as for the mask: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery

Perhaps with higher thresholds the clusters become smaller. Or instead of looking at the percentages, you could just open the thresholded map overlaid on the MNI T1 image, and name the structures as you identify them visually.

Hope this helps!

All the best,

Anderson



2013/5/8 Bonnie Lam <[log in to unmask]>
Dear FSL users,

I have been using the autoaq command and get the following output (as below).

The atlas query website suggested the number indicated is a number from 0-100 and can be interpreted as percentages.  So it indicates how probable the tract is affected if I am using an white matter atlas in this case? 

I do realized it does not add up to 100 and the each number is relatively small (mostly less than 1), therefore, I am not sure how exactly should I be interpreting this.

I would be grateful if anyone can shed some light on this.

Thanks,
Bonnie


Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
1 49015 0.999 -11 28 -10 -1.21 -2.72 15.1
==========================================
Structures to which each cluster peak belongs to:
-1.21,-2.72,15.1,JHU White-Matter Tractography Atlas,No label found!
==========================================
Structures to which each cluster belongs to:

Cluster #1
Anterior thalamic radiation L:1.57023
Anterior thalamic radiation R:0.961991
Corticospinal tract L:0.401183
Corticospinal tract R:0.172784
Cingulum (cingulate gyrus) L:0.66753
Cingulum (cingulate gyrus) R:0.336693
Cingulum (hippocampus) L:0.0125676
Cingulum (hippocampus) R:0.0311741
Forceps major:0.576497
Forceps minor:4.75193
Inferior fronto-occipital fasciculus L:1.87979
Inferior fronto-occipital fasciculus R:2.00002
Inferior longitudinal fasciculus L:1.0455
Inferior longitudinal fasciculus R:1.06078
Superior longitudinal fasciculus L:2.07728
Superior longitudinal fasciculus R:1.4285
Uncinate fasciculus L:1.0639
Uncinate fasciculus R:0.515352
Superior longitudinal fasciculus (temporal part) L:0.936081
Superior longitudinal fasciculus (temporal part) R:0.466


From: "Nucleos P" <[log in to unmask]>
To: [log in to unmask]
Sent: Thursday, April 4, 2013 8:31:25 AM
Subject: Re: [FSL] autoaq atlas query


Hi Christophe -

Thank you very much!

Best,
Catherine


On Wed, Apr 3, 2013 at 4:43 PM, Christophe Bedetti <[log in to unmask]> wrote:
Hi Catherine,

You can find it from the blog of the author with a lot of other useful brain imaging information.

Christophe


On 3 April 2013 14:14, SUBSCRIBE FSL Nucleos <[log in to unmask]> wrote:
Hello FSLers,

Where can I find the autoaq script? I would like to add this to my bin.

Thanks,
Catherine





--

Bonnie Yin Ka Lam
PhD Candidate



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