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-1.0.2) - 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.
- 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="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 thetemplates
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 thetemplates
subdirectory in yourStructuralQC-x.y.z
folder on your system. The script will copy reference files (S900* and mean MNI152 T1 atlas target) to yourOutputFolder
, so that the scenes can find them.
-
Enter this command at a terminal window:
bash GenerateStructuralScenes.sh
-
Confirm the scenes were generated:
cd $StudyFolder ls
There should be one scene file for each subject in
SubjList
. (Each of which contains multiple scenes available for showing inwb_view
). -
View the scene file using wb_view:
wb_view "$Subject".structuralQC.wb.scene