This script is so useful! It should be shared to everyone.

On Wed, Feb 13, 2013 at 9:02 PM, David Gutman <[log in to unmask]> wrote:

So there's a post by Anderson Winkler on the 8th of this year that included a script (reattached-- thanks Anderson, this looks useful) that helped to automate some of those lookups.

Also--- this topic made me start playing around again with atlasquery... and I noticed it doesn't seem to be showing up on my recently installed Ubuntu 12.04 system ....

A quick search seems to suggest it's included in the fsl-4.1 version, but maybe not the 5.0 Ubuntu package...and at least on my system the 4.1 installation simply created a a symbolic link to a directory that doesn't exist....   

apt-file search atlasquery  yielded:   fsl-4.1: /usr/lib/fsl/4.1/atlasquery

Then when I checked the installed file...

 ls -al /usr/lib/fsl/4.1/atlasquery 

/usr/lib/fsl/4.1/atlasquery -> ../../../bin/atlasquery

---------- Forwarded message ----------

From: Anderson M. Winkler <[log in to unmask]>

Date: Tue, Jan 8, 2013 at 2:51 PM

Subject: Re: [FSL] FSL VBM result reports

To: [log in to unmask]

On Wed, Feb 13, 2013 at 7:22 PM, zhang mingxia <[log in to unmask]> wrote:

Hi Mark,

I have one more question of atlasquery. If the mask has more other one clusters, it is not recommended to use the -m option, right? Because atlasquery will average all voxels in the mask, we can't get the name of every cluster, right?

Mingxia 

On Wed, Feb 13, 2013 at 1:54 PM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

This is explained at:

  http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery

All the best,

Mark

On 13 Feb 2013, at 21:52, Sandra Petris <[log in to unmask]>

 wrote:

Hi Fsl experts,

when I run the following:

atlasquery -a "JHU White-Matter Tractography Atlas" -m cluster_index_t3_085

I get the following and I would like to know what means the number near the atlas name.

thanks alot

sandra

Anterior thalamic radiation L:1.09575

Anterior thalamic radiation R:0.0030888

Corticospinal tract L:6.02214

Corticospinal tract R:0.123295

Cingulum (cingulate gyrus) L:0.0780352

Forceps minor:0.511154

Inferior fronto-occipital fasciculus L:2.84736

Inferior longitudinal fasciculus L:0.944402

Superior longitudinal fasciculus L:7.9619

Superior longitudinal fasciculus R:0.020592

Uncinate fasciculus L:0.0123552

Superior longitudinal fasciculus (temporal part) L:3.10425

Superior longitudinal fasciculus (temporal part) R:0.00669241

--
David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine