Scene Generation

Scene Generation

Copy the following files to a subject folder within a new derivatives folder named slicer_scene:

derivatives/
    └── atlasreg/
        └── sub-<subject_label>/
                ├── qc/...
                ├── sub-<subject_label>_acq-contrast_T1w.nii.gz
                ├── sub-<subject_label>_acq-noncontrast_space-T1w_desc-affine_T1w.nii.gz
                ├── sub-<sub_label>_space-T1w_desc-rigid_ses-post_ct.nii.gz
                ├── sub-<sub_label>_acq-nac_space-T1w_desc-rigid_pet.nii.gz
                ├── sub-<sub_label>_acq-ac_space-T1w_desc-rigid_pet.nii.gz
                ├── sub-<sub_label>_desc-rigid_from-noncontrast_to-contrast_type-ras_xfm.tfm
                ├── sub-<sub_label>_desc-nonlin_atlas-CerebrAThomasMiddle_from-MNI152NLin2009cSym_dseg.seg.nrrd

Within 3D Slicer, create the following markups lists and save them in the slicer_scene subject folder:

derivatives/
    └── slicer_scene/
        └── sub-<subject_label>/
                ├── sub-<sub_label>_acpc.fcsv
                ├── sub-<sub_label>_actual.fcsv
                ├── sub-<sub_label>_planned.fcsv
                ├── sub-<sub_label>_SEEGA.fcsv
                ├── ...