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]
#
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