Changes between Version 16 and Version 17 of barSoftwareGUI


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Timestamp:
10/16/11 12:48:29 (13 years ago)
Author:
pmajka
Comment:

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  • barSoftwareGUI

    v16 v17  
    9898Apart 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:: 
    9999 
    100   $./batchreconstructor.sh 
     100  $./batchinterface.sh 
    101101   
    102102  Usage: ./batchinterface.sh [options] <CAF index> [<structure 1> [<structure 2> ...]] 
    … …  
    146146The 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: :: 
    147147 
    148 $./batchreconstructor.sh ~/atlases/mouse/caf/index.xml Thalamus --exportToNiftii 
     148$./batchinterface.sh ~/atlases/mouse/caf/index.xml Thalamus --exportToNiftii 
    149149 
    150150By 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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