New Example using the VSD database.

[MCM-Fischer]

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[modenaxe]

Thank you @MCM-Fischer - sorry if this is taking ages! @renaultJB so you have time to review the proposed fix to the STAPLE-Talus algorithm?

[renaultJB]

Thank you @MCM-Fischer and @modenaxe, I will review it this weekend 😃

[MCM-Fischer]

@modenaxe No problem ;-). Maybe it makes more sense if I push the talus fix separately to the main branch?

[modenaxe]

@MCM-Fischer I think it would be indeed easier to manage and merge, please tag @renaultJB if you do so he's updated as well

[modenaxe]

Hi @MCM-Fischer I am finally back to this. I have pushed to your repository a new proposed location for the example, in the msk-STAPLE\advanced_examples\process_VSD_dataset folder. Comments/reasons:

1. your script downloads the VSD dataset, that is relatively large compare to the size of STAPLE
2. the script requires matGeom. Is it possible to donwload that from GitHub as you do for the VSD dataset?
3. I would place both packages in the same folder, checking them out without git history git clone --depth 1 to minimise the download.

I think the example is great but I want to keep the dependencies and size of the main package minimal (both for users benefit and for our benefit in maintenance). @renaultJB do you agree?

@MCM-Fischer have you published the dataset paper as well?

Thank you,

Luca

[modenaxe]

Also, @MCM-Fischer I have merged the main branch (with your talus fixes) to the VSD branch with the example but I still have issue processing some datasets, e.g. VSD_010_L. Could you please double check the code is properly integrated?

[MCM-Fischer]

Also, @MCM-Fischer I have merged the main branch (with your talus fixes) to the VSD branch with the example but I still have issue processing some datasets, e.g. VSD_010_L. Could you please double check the code is properly integrated?

Should be fixed with Pull request #117

[MCM-Fischer]

Hi @MCM-Fischer I am finally back to this. I have pushed to your repository a new proposed location for the example, in the msk-STAPLE\advanced_examples\process_VSD_dataset folder. Comments/reasons:

1. your script downloads the VSD dataset, that is relatively large compare to the size of STAPLE

2. the script requires [matGeom](https://github.com/mattools/matGeom). Is it possible to donwload that from GitHub as you do for the VSD dataset?

3. I would place both packages in the same folder, checking them out without git history `git clone --depth 1` to minimise the download.

I think the example is great but I want to keep the dependencies and size of the main package minimal (both for users benefit and for our benefit in maintenance). @renaultJB do you agree?

Hi Luca

I've kept the VSD example in the main folder because it would not fit to the description in the README.md of the advanced examples. It is actually a one-click (Run F5) example now. VSD and matGeom are downloaded. However, the git history of the two repositories is deleted afterwards. No additional dependencies are created. VSD and matGeom folders have been added to .gitignore.

Kind regards

[MCM-Fischer]

@MCM-Fischer have you published the dataset paper as well?

Hi Luca

Yes, finally it was published now: Fischer, M.C.M. Database of segmentations and surface models of bones of the entire lower body created from cadaver CT scans. Sci Data 10, 763 (2023). https://doi.org/10.1038/s41597-023-02669-z

Kind regards

[modenaxe]

Hi @MCM-Fischer thank you for contributing with this example! I should have time to review this hopefully before the holiday break - thank you for your patience!

[MCM-Fischer]

Hi Luca At first please merge #117. Kind regards