Okay so you clearly have the atlases installed and atlasquery can find them.

Can you copy and paste the exact command line you are using along with the output?

Perhaps also send a screenshot just to make sure. Feel free to send the screenshot to my email directly as it might be too big for the list.

On Mon, Mar 9, 2015 at 5:07 PM, Archana Malagi <[log in to unmask]> wrote:

Hi Niels,

Yes, both the scripts giving the output as given:

Test: <b>JHU White-Matter Tractography Atlas</b><br>11% Anterior thalamic
radiation R

Thanks,
Archana





# Can you try downloading these two small test scripts and run them?
#
# e.g.
#
# chmod a+x test_atlasquery.sh
# chmod a+x test_atlasquery.tcsh
#
# ./test_atlasquery.sh
# ./test_atlasquery.tcsh
#
# They should both output the following:
#
# Test: <b>JHU White-Matter Tractography Atlas</b><br>11% Anterior thalamic
# radiation R
#
# On Thu, Mar 5, 2015 at 3:27 PM, Archana Malagi <[log in to unmask]> wrote:
#
#> Hi Paul,
#>
#> Operating system which i am using is CentOS-6 (64-bit).
#>
#> I installed fslinstaller.py and then followed instruction as given in
#> this
#> link http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux. And
#> then
#> i set path in tsch shell.
#>
#> If i try different atlas same error appears.
#>
#> Thanks,
#> Archana
#>
#>
#>
#> # Hi Archana,
#> #
#> # This is a strange problem - could you tell me what operating system
#> you
#> # are
#> # using, and how you installed FSL?
#> #
#> # What happens if you try a different atlas, e.g. "MNI Structural Atlas"
#> ?
#> #
#> # Thanks,
#> #
#> # Paul
#> #
#> # On Thu, Mar 5, 2015 at 12:06 PM, Archana Malagi <[log in to unmask]>
#> # wrote:
#> #
#> #> Hi Paul,
#> #>
#> #> FSL version which i am using is 5.0.7 and the output given by
#> atlasquery
#> #> is :
#> #> atlasquery -a ¨JHU White-Matter Tractography Atlas¨ -m
#> #> mask_size2.nii.gz
#> #>
#> #> Invalid atlas name. Try one of:
#> #>
#> #> Cerebellar Atlas in MNI152 space after normalization with FLIRT
#> #> Cerebellar Atlas in MNI152 space after normalization with FNIRT
#> #> Harvard-Oxford Cortical Structural Atlas
#> #> Harvard-Oxford Subcortical Structural Atlas
#> #> JHU ICBM-DTI-81 White-Matter Labels
#> #> JHU White-Matter Tractography Atlas
#> #> Juelich Histological Atlas
#> #> MNI Structural Atlas
#> #> Mars Parietal connectivity-based parcellation
#> #> Mars TPJ connectivity-based parcellation
#> #> Neubert Ventral Frontal connectivity-based parcellation
#> #> Oxford Thalamic Connectivity Probability Atlas
#> #> Oxford-Imanova Striatal Connectivity Atlas 3 sub-regions
#> #> Oxford-Imanova Striatal Connectivity Atlas 7 sub-regions
#> #> Oxford-Imanova Striatal Structural Atlas
#> #> Sallet Dorsal Frontal connectivity-based parcellation
#> #> Subthalamic Nucleus Atlas
#> #> Talairach Daemon Labels
#> #>
#> #>
#> #>
#> #> # Hi Archana,
#> #> #
#> #> # What version of FSL are you using? Could you please give the full
#> #> output
#> #> # that atlasquery gives when you run it?
#> #> #
#> #> # Thanks,
#> #> #
#> #> # Paul
#> #> #
#> #> # On Thu, Mar 5, 2015 at 4:00 AM, Archana Malagi <[log in to unmask]>
#> #> wrote:
#> #> #
#> #> #> Hi FSL experts,
#> #> #>
#> #> #> I am facing problem while using command atlasquery. I have
#> generated
#> #> #> mask
#> #> #> of significant clusters formed by randomise command,
#> #> #>
#> #> #> atlasquery -a "JHU White-Matter Tractography Atlas" -m
#> #> mask_size2.nii.gz
#> #> #>
#> #> #> Error given is invalid atlas name used, is there any error in this
#> #> #> command?
#> #> #>
#> #> #> Thanks,
#> #> #> Archana
#> #> #>
#> #> #
#> #>
#> #
#>
#
#
#
# --
# Niels Bergsland
# Integration Director
# Buffalo Neuroimaging Analysis Center
# 100 High St. Buffalo NY 14203
# [log in to unmask]
#

--

Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]