Generating Workbench Scenes for Structural Quality Control
Authors: Michael Harms and Donna Dierker
-
Download the
StructuralQC-x.y.z.zip
archive from GitHub:- Visit: https://github.com/Washington-University/StructuralQC/releases
- Under
Downloads
choose theSource code (zip)
link for the latest release - The resulting
.zip
file will be namedStructuralQC-x.y.z
wherex.y.z
reflects the version number.
-
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.
- a single script --
- You will probably invoke the script multiple times (i.e., for different batches of subjects).
- The resulting subdirectory will be named
-
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 thetemplates
subdirectory in yourStructuralQC-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.
- If set to the empty string (
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
$TemplatesFolder
, and uses that for creating the scene.
- If TRUE, the script will copy reference files (S1200* and mean MNI152 T1 atlas target) to
-
Enter this command at a terminal window:
bash GenerateStructuralScenes.sh
-
Confirm the scenes were generated in
OutputSceneFolder
. -
View the scene file using wb_view:
wb_view "$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.