Washington-University / StructuralQC

Description

Generating Workbench Scenes for Structural Quality Control

Authors: Michael Harms and Donna Dierker

Use

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-1.2.0)
   • 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="SubjID1 SubjID2 SubjID3"
   TemplatesFolder="/location/of/unpacked/StructuralQC/templates"
   StudyFolder="/location/of/subject/data/directories"
   OutputSceneFolder=SEE_BELOW
   CopyTemplates=TRUE or FALSE
   
   

   • SubjList is a space delimited list of subject ID's to be processed.
   • TemplatesFolder is the location of the templates subdirectory in your StructuralQC-x.y.z folder on your system.
   • StudyFolder is the directory containing the subject data (organized in standard ConnectomeDB file structure).
   • OutputSceneFolder controls where the per-subject scenes (and a small number of other created files) get saved.
     • If set to the empty string (""), the files for each subject will go into their $StudyFolder/$Subject/MNINonLinear/StructuralQC directory. Obviously, this requires that you have write permission into the $StudyFolder tree!
     • Otherwise, it specifies the "common" directory where the scene files go for all subjects.
   • CopyTemplates
     • If TRUE, the script will copy reference files (S1200* and mean MNI152 T1 atlas target) to OutputSceneFolder (per the interpretation provided above), and use the copies at that location in the scene.
     • If FALSE, the script determines the relative path to $TemplatesFolder, and uses that for creating the scene.

4. Enter this command at a terminal window:

   bash GenerateStructuralScenes.sh
   

5. Confirm the scenes were generated in OutputSceneFolder.

6. View the scene file using wb_view:

   wb_view "$Subject".structuralQC.wb.scene
   

   Note that each scene file actually contains multiple scenes available for showing in wb_view. Each individual scene contains a brief description of its contents within the Scenes window.