single-file segmentation DICOM (examples in the RIDER Lung data from TCIA
[zip file]) is recognized on import,
Modality: SEG in the Slicer DICOM browser;
a dialog appeared to suggest I get the
Quantitative Reporting module...
- Extension Manager can be opened by clicking the
“E” icon on Slicer window top right.
- QuantitativeReporting depends on other extensions: PETDICOMExtension,
DCMQI, SlicerDevelopmentToolbox, so I clicked to install them all.
Upon Slicer quit/restart, the segmentations were loaded successfully into
the viewer. The example data folder included 2 scans "4" and "8"
and a bunch of segmentations, which were aligned to "4" ("8" was offset).
In the Volumes module I could delete "8", leaving just the one aligned
with the segmentations.
I tried making my own segmentation in Slicer, as in this
video
tutorial. There are lots of options, including those analogous to
Volume Eraser and Hide Dust. Segmentation save format is only NRRD,
and export format choices are only STL and OBJ.
Saved NRRD file
could be read back in, and was automatically listed as a segmentation.
Exported STL file
(coordinate system choices LPS or
RAS, I chose the default LPS) could be read back in,
but was listed as a separate model, not a segmentation, and was not aligned.
1/19/2019
In the RIDER Lung segmentation DICOM file metadata, manufacturer and
software version refer only to Slicer, but the manufacturer model field
gives the URL for the
Quantitative Reporting module, which sounds like
it can save DICOM segmentations. I couldn't use it to save the
segmentation opened from previously saved NRRD (error: empty segmentation),
but I could save one made in the current session or one previously read from
DICOM (RIDER Lung). However, “saving” in this context only
means adding it to the internal Slicer DICOM database (SQL), where the RIDER
lung segmentation was already. Since the database contents persist through
quitting/restarting Slicer, this process at least allows saving my
segmentation for later use in Slicer, but doesn't produce a file that
can be used in some other program. The Slicer database dialog has an
Export button for writing DICOM, but its balloon help says
“not yet available” (even in daily build 1/18/2019) and trying
to use it anyway gives “Error occurred in exporter” message.
I see another
video tutorial showing a different set of steps for
saving segmentations + volume to DICOM.
I followed that entire workflow which worked up to clicking the Export
button, which did absolutely nothing, as far as I could tell.
However, in the video looks like I need a DicomRtImportExport plugin or
something like that. I didn't find exactly that plugin name, but I installed
one named SlicerRT
(and TCIABrowser too since it interested me).
Restarted, repeated the entire process, still got error or nothing exported.
1/20/2019 Got a little farther: if I choose export format RT,
I can export a study “to DICOM” using the workflow
shown in that video, but only to the Slicer DICOM database and only
as modality RTSTRUCT, not SEG. Export type DICOMSegmentation seems
to either cause error or do nothing, export type Scalar Volume only
exports the images, not the segmentation. Again, no actual DICOM
output files, only export to the Slicer DICOM database.
The only way I found to get SEG into the database is with the
Quantitative Reporting module, as reported above.