Yes - due to the "diluted percentages" as Anderson said, we used the
autoaq output as a "guide" when looking at the thresholded mask over
the MNI152 brain where the visualization made the results more clear.

I have found the script helpful for our probabilistic tractography analyses.

On 5/8/13, Anderson M. Winkler <[log in to unmask]> wrote:
> 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.
>>> http://brainder.org/2012/07/30/automatic-atlas-queries-in-fsl/
>>>
>>> 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
>>
>>
>>  www.NeuRA.edu.au  <http://neura.edu.au/>
>> Barker Street Randwick Sydney NSW 2031 Australia
>> PO Box 1165 Randwick Sydney NSW 2031 Australia
>> *T* +61 2 9399 1112
>>
>>
>