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Hello - I have been trying to use the autoaq script and this is the message I get: autoaq -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 -o text -a "JHU White-Matter Tractography Atlas" if: Expression Syntax. What am I doing wrong? Thanks, Cat On 2/14/13, Anderson M. Winkler <[log in to unmask]> wrote: > Feel free to use and share it. Hope it helps! > Anderson > > > 2013/2/14 zhang mingxia <[log in to unmask]> > >> 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 >>> >> >> >