Nice leg dataset - could be used for atlas

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.

https://wiki.cancerimagingarchive.net/display/Public/TCGA-HNSC#118295898f30f3d924e54ae8bfee4fb5ac9fcb5e

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. http://doi.org/10.7937/K9/TCIA.2016.LXKQ47MS

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.