Changes between Version 13 and Version 14 of barSoftwareGUI


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Timestamp:
10/12/11 13:47:02 (13 years ago)
Author:
pmajka
Comment:

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  • barSoftwareGUI

    v13 v14  
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    101 Apart from GUI, |3dBAR| comes with command line interface (or shorter: CLI) allowing the user to perform batch reconstructions without configured graphics environment. 
    102  
    103 :: 
     101Apart from GUI, |3dBAR| comes with command line interface (or shorter: CLI) allowing the user to perform batch reconstructions without configured graphics environment. After invoking the batch interface, following information will appear:: 
    104102 
    105103  $./batchreconstructor.sh 
    … …  
    147145 
    148146 
     147The ``<CAF index>`` is a location of the index file of the given CAF dataset while the ``[<structure 1> [<structure 2> ...]]`` is space-separated list of all structures to reconstruction contained in the CAF dataset. 
     148 
     149The simplest usage of the CLI is to generate reconstruction of a single structure from provided CAF dataset using default settings. Assume that our CAF dataset is located in the ``~/atlases/mouse/caf/`` directory and we would like to reconstruct the *Thalamus* as save a nifti volume with the reconstruction: :: 
     150 
     151$./batchreconstructor.sh ~/atlases/mouse/caf/index.xml Thalamus --exportToNiftii 
     152 
     153By default, the reconstructions generated using a predefined pipeline and stored in directory parallel to the CAF dataset directory (in this example it would be ``~/atlases/mouse/reconstructions/``). However, this behavior can be customized using various switches.  
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    150156.. |figA| image:: http://www.3dbar.org/raw-attachment/wiki/barSoftwareManualIndex/3dbar_interface_strucure_selection.png 
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