Here’s a nrrd file of a CT leg at nice resolution (.7 x .7 x .3 mm) voxels.
The link above is just the left leg, but both legs and more pelvic anatomy is available in the original DICOM data. It is shared under a CC-by attribution license and the original is on TCIA. Be sure to cite the data source if you use it.
The data is for subject TCGA-CV-A6JU in the TCGA-HNSC collection.
Looks nice thanks @pieper . This is the collection right? TCIA Collections - The Cancer Imaging Archive (TCIA)
Yes, this one specifically. Be sure to cite it if you use the data in any publications.
hi , i have downloaded your file in .nrrd format and looked at the image in slicer. it’s amazing. if I want to cite it, I just need to cite the TCGA-HNSC collection as a whole or do I need to cite the specific patient as well?
also, I tried to download the file from the cancer research website, do you use this one?
TCGA-HNSC> TCGA-CV-A6JU > 03 feb 2001 data set > CTA LOWER EXTREM W&W/O > SCOUT.
I know its quite late but I’m doing a force distribution fea on knee. i would appreciate if you can reply so I can cite this as healthy knee.
Glad the data is useful for you. I believe it’s enough to cite these two papers. We don’t know who the patient is, but also mentioning the subject ID is good (TCGA-CV-A6JU).
Zuley, M. L., Jarosz, R., Kirk, S., Lee, Y., Colen, R., Garcia, K., … Aredes, N. D. (2016). Radiology Data from The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma [TCGA-HNSC] collection. The Cancer Imaging Archive. TCGA-HNSC - The Cancer Imaging Archive (TCIA)
Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper)
It’s not the scout image, but it’s another series with 3000 slices and starts about the waist and includes both legs.
im trying to create a 3d volume out of it, but the threshold doesn’t select the whole bone. when i satisfied with a threshhold it has other debree around it which i wont want. ofc i can remove it but it will take ages any working around it?
Have a look at the WrapSolidify tool and related discussions.
Hi @pieper, I am looking for CT volumetric data of knee. The link you shared takes me to a head-neck data. I was wondering if the knee data is available now. If you have updated information, please share.
The dropbox link above is to the leg data. It comes from a collection of data related to head and neck cancer, but sometimes whole body scans are performed and that’s why this case happened to have the lower extremity.
Dear Dr. Pieper @pieper,
Thank you very much for sharing the NRRD file. I was able to load and inspect the data successfully.
I wanted to ask if there are any additional NRRD files of legs from other patients that could be used for testing. This would be very helpful for validating the experiments.
Thank you again for your support.
Unfortunately there’s not currently and inventory of which body parts are visible in which scans, but I’m sure there are other leg scans available. If you have time and resources you could just do bulk downloads and run one of the body segmentation tools, like TotalSegmentator to find which parts are visible in the scans.
Thank you very much for your reply and for the helpful suggestion.
I am specifically looking for additional CT or CTA scans (cross-section) that include the lower limbs from more different people, to use only for testing and validation. Even a small number of such scans would be sufficient.
Thank you also for the suggestion to use bulk downloads with a body segmentation tool such as TotalSegmentator; this is very helpful.
Just to mention that this is a practical approach, I had about 500 CTs and I wanted ones with pelvis included so I ran TotalSegmentator on all of them and picked the ones where a femur had been selected and got 60 or so that all included the pelvis. No false positives.
May be this one could be helpful.
thi is so great scans thanks a lot !! how to cite in case I got lucky and somehow able to publish my work?
You may cite the Slicer forum if a citation is mandatory.
