VMR Preprocessing Sub-Workflow
In order to preprocess the anatomical data set of each subject, the Preprocessing Workflow Definition dialog is re-entered and the VMR Preprocessing sub-workflow is selected. The appearing document input list shows the "ses-01_T1w" document that is selected for anatomical preprocessing. The right side shows the available options that are kept as specified, i.e. the Extract Brain From Head Tissue option (default on) will extract the brain by removing other head tissue and the Correct Intensity Inhomogeneities option will reduce spatial intensity inhomogeneities in the 3D volumes. The Rescale Resolution (Iso-Voxel) option is not checked since the VMR document has already a resolution of 1mm x 1mm x 1mm.
At this point one could also include the VMR Normalization workflow but the document input list will show only the unpreprocessed document in the current version of the program (this will be changed in a future update). In case that the preprocessed document is intended to serve as input for the VMR normalization sub-workflow, it is currently necessary to first specify the VMR preprocessing workflow by clicking the OK button of the dialog. The dialog can then be re-entered without having to run the VMR preprocessing workflow since now the expected generic name will be available when selecting the VMR Normalization workflow (see next topic).
The screenshot above shows the VMR preprocessing workflow in the Workflows table (entry 6) with the generic input name in the Input column and the generic preprocessed name in the Output column.
The screenshot above captures a moment during anatomical preprocessing. The logged information in the Log tab reveals that at this time point intensity inhomogeneity correction was performed for the anatomical data set of subject 2 ("sub-02"). At the begin of the logged information, the anatomical preprocessing parameters are shown which are also stored in the "parameters.json" file inside the respective workflow folder with the name "workflow_id-6_type-2_name-anatpreprocessing". Note that the preprocessed output files will be stored both in 8-bit (VMR) and 16-bit (V16) format as indicated in the screenshot below.
Copyright © 2020 Rainer Goebel. All rights reserved.