Hello everyone, I am new to 3DSlicer and I am working on a lower body MRI study with the goal of segmenting 35 muscles and creating 3D visualizations from the segmentations. Manual muscle segmentations have been completed using Dafne. Dafne was originally chosen over 3DSlicer as its software is designed specifically for lower body muscle segmentation.
I would now like to view the masks created in Dafne in 3DSlicer. After exporting the masks from Dafne as DICOM files and importing them to 3DSlicer, they do not appear to be visible.
Additionally, the original MR images were taken in batches, and each 111-image batch contains a 5–6 slice overlap with the adjacent batch. When I import them into Slicer, I have to view each batch separately as different image sets.
Therefore I have a few questions:
Would it be possible to view these imported masks in 3DSlicer to create 3D models of each individual muscle?
Is there a way to merge the separate MRI batches into a single continuous volume so I can scroll seamlessly from the hip to the foot, rather than switching between different image sets?
I don’t know if anyone here has used Dafne, but if it can put out standard DICOM Segmentation Objects, then Slicer should be able to load them if you install the Quantitative Reporting extension.
For the other question this module in the Sandbox extension might do what you want:
Thank you for your response, Steve. The Sandbox extension worked for the original DICOM images.
However, I have not been able to load the segmentation masks. If possible, could you direct me to material outlining how to import these DICOM Segmentation Objects into Quantitative Reporting? This tutorial mainly focuses on how to segment once the images are loaded. Thank you.
If the dicom segmentations are recognized by Quantitative Reporting they should just load so there’s no specific tutorial. SEG is complex, so probably there’s something incompatible (maybe valid data that differs in details or something non-standard).
I see you filed an issue on github, which is good.
Probably you’ll need to post example data. Also it could help you to try this tool: DICOM Validator - dciodvfy
Thank you for the information, Steve. I have been in contact with Andriy and he provided me with a solution. He suggested I download the masks from Dafne in NIfTI format and import the data as a segmentation. It has worked and I can now view the masks in 3D! Thank you for your help and I may have more questions as I continue learning the intricacies of 3DSlicer!
To add to that, I suggested trying NIfTI because that option was shown in the screenshot shared by @trumanchiu, and I didn’t want to risk the exposure of patient information in the DICOM files that the system was exporting, since the user did not have experience with de-identification. It would still be interesting to see what was the issue in the DICOM that Dafne is exporting, but not some other time.
I have a few questions regarding refining individual muscle/bone segmentations and also exporting to 3D viewers.
In terms of muscle segmentations, unfortunately due to a glitch in Dafne, the software we used to create the segmentation masks, we had an issue with our interpolating which created extra masks that you can see in the images below on the left. Is there a way to quickly remove these masks? I tried using the “Islands” function but when I am not able to use a minimum size that preserves the smaller segmentations done while removing the strips on the left.
^ Just the vasti muscles with the extra masks on the left
In addition to removing the extra masks, I have been using the “Segment Editor” function, particularly the “Fill between slices” function. I’ve shown an example below. Is there a way to edit the results of the interpolation?
^ For example, in this axial segmentation of the proximal femur, I am unable to edit the “results”. Instead, I would have to segment over top of it and the auto-update feature removes that initial mask.
In terms of 3D visualization, I have exported individual muscle in .stl format. I have viewed them on 3D Viewer. However, we are looking for a way to export all 35 muscles together, and be able to select which muscles you want to view in a common, user-friendly platform. The goal is for participants of the study to view their segmented muscles without having to use a platform like 3D Slicer. Is there a platform that this is able to be done in?In addition to this, is there a way to compress these files? One model (VMO) is already ~11 MB.
You can probably fix all the segmentation errors with tools like scissors. For the fill between slices you may need to segment the femur first and then nave it not overwrite that segment.
For easy web viewer software you can export to gltf using the OpenAntatomy extension. There are lots of viewers on the web to pick from.
Do you know how I would be able to categorize my segmentations like the first photo below? The second photo is what is looks like when I put all of the segmentations in 1 folder as it would not let me import different 3D models at the same time in 3D Viewer. Thanks.
