Hi Anderson -
I tried it once more and it works! I'm really excited about this
script. Thank you!!!
-Cat
On 4/5/13, Anderson M. Winkler <[log in to unmask]> wrote:
> Hi Cat,
> Could you please type "ls -l /bin/bash", then copy output you get and paste
> it here?
> Thanks!
> Anderson
>
>
>
> 2013/4/5 Nucleos P <[log in to unmask]>
>
>> 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
>> >>>
>> >>
>> >>
>> >
>>
>
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