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Generating Workbench Scenes for Structural Quality Control

Authors: Michael Harms and Donna Dierker

1. Download the StructuralQC-x.y.z.zip archive from GitHub:

   • Visit: https://github.com/Washington-University/StructuralQC/releases
   • Under Downloads choose the Source code (zip) link for the latest release
   • The resulting .zip file will be named StructuralQC-x.y.z where x.y.z reflects the version number.

2. Unzip the archive in a directory where you have read and write permission.

   • The resulting subdirectory will be named StructuralQC-x.y.z (e.g., StructuralQC-1.0.2)
   • The StructuralQC-x.y.z directory will contain:
     • a single script -- GenerateStructuralScenes.sh and
     • a templates directory that contains files that are needed to render the scenes.
   • You will probably invoke the script multiple times (i.e., for different batches of subjects).

3. Use a text editor to edit the following variables in the GenerateStructuralScenes.sh script:

   SubjList="176239 199958 415837 433839 943862 987983"
   OutputFolder="/location/of/my/QC/output/directory"
   StudyFolder="/location/of/subject/data/directories"
   TemplateFolder="/location/of/unpacked/StructuralQC/templates"
   

   • SubjList is a space delimited list of subject ID's to be processed.
   • OutputFolder is where you want the per-subject scenes (and copies of the files in the templates directory) to be located.
   • StudyFolder is the directory containing the subject data (organized in standard ConnectomeDB file structure). It is used to replace a dummy string in the template scene so that the generated per-subject scene file can find the necessary file inputs.
   • TemplateFolder is the location of the templates subdirectory in your StructuralQC-x.y.z folder on your system. The script will copy reference files (S900* and mean MNI152 T1 atlas target) to your OutputFolder, so that the scenes can find them.

4. Enter this command at a terminal window:

   bash GenerateStructuralScenes.sh
   

5. Confirm the scenes were generated:

   cd $StudyFolder
   ls
   

   There should be one scene file for each subject in SubjList. (Each of which contains multiple scenes available for showing in wb_view).

6. View the scene file using wb_view:

   wb_view "$Subject".structuralQC.wb.scene