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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. >> 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 > >