Upload pre-processing sample data

[amymmorton]

@jcfr could you remind me the best location/mechanism for complementary sample data upload that includes preprocessing data?

[amymmorton]

@jdholt04 could you confirm that the sample data has all preprocessing data?

[jdholt04]

@amymmorton The three sample datasets have all of the necessary preprocessing data, except anonymized DICOMs or an .nrrd file that would be needed for users to segment and generate partial volumes.

[amymmorton]

John, could you please see if you can determine the source dataset for the original knee sample data? ([see here]( https://github.com/BrownBiomechanics/Autoscoper/tree/main/sample_data)) But if you're spinning your wheels- we can pivot to a different dataset. Thanks

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On Mon, Jan 13, 2025 at 3:29 PM John Holtgrewe ***@***.***> wrote: @amymmorton <https://github.com/amymmorton> The three sample datasets have all of the necessary preprocessing data, except anonymized DICOMs or an .nrrd file that would be needed for users to segment and generate partial volumes. — Reply to this email directly, view it on GitHub <#138 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUUPFQRQELPTYBX6MCBHFT2KQO4LAVCNFSM6AAAAABRFCUTLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOBYGEZTCMZVGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- ----------- Amy Morton MSc *Senior Research Engineer - Software* *Brown University Healt**h* Orthopaedic Research, 1 Hoppin Street, Coro West, 4th Providence, RI 02903-4923 linkedin <https://www.linkedin.com/in/amy-morton-35374340/>

[jdholt04]

The sample dataset that can be downloaded in Slicer doesn't seem to match the dataset in the link. I did find the source of the dataset that can be downloaded from Slicer. Should I attach the .nrrd file here or is there another spot I should upload it to?

[amymmorton]

I would advise upload a copy to the shared gdrive and link here. Thanks

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On Tue, Jan 14, 2025 at 12:27 PM John Holtgrewe ***@***.***> wrote: The sample dataset that can be downloaded in Slicer doesn't seem to match the dataset in the link. I did find the source of the dataset that can be downloaded from Slicer. Should I attach the .nrrd file here or is there another spot I should upload it to? — Reply to this email directly, view it on GitHub <#138 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUUPFW4V4JIXT2CZ3K33WT2KVCHHAVCNFSM6AAAAABRFCUTLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOJQGYZTOMJVGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- ----------- Amy Morton MSc *Senior Research Engineer - Software* *Brown University Healt**h* Orthopaedic Research, 1 Hoppin Street, Coro West, 4th Providence, RI 02903-4923 linkedin <https://www.linkedin.com/in/amy-morton-35374340/>

[jdholt04]

https://drive.google.com/drive/folders/14LtstqHeILYnRdkVMqYdN7SBiqd9TJen?usp=drive_link

[amymmorton]

With the augmented pre-processing module , which now allows full bvr workup and cfg generation.. It's important to provide relevant and appropriately compliant data .
The wrist, knee and ankle data have some missing elements and were created prior to implemented standards.

All datasets require:.nrrd source CT from which partial volumes were (and can be) created. 
I advise we recreate all partial volume tiff stacks (and recreate tfm files in Transform folders , also to be included)  which will also mean either: retracking the cropped versions or applying transforms to tra outputs to appropriately reflect the cropped partial volumes. 

One off issues have already been created to rename non-standard folders (Radiographs-> RadiographImages, Meshes-> Models)

[amymmorton]

Wrist Sample Data (no tracking tra)
This is the exact same subject and movement previously available on SampleData but processed with the Pre Processing module , includes Transforms, Volumes and AUT'bone'.stl

*** TODO - add more robust error checking in the Partial Volume Preprocessing step for checking contents of the existing folders. **** (I'll add this in another issue)

[jdholt04]

@sbelsk

https://drive.google.com/drive/folders/14LtstqHeILYnRdkVMqYdN7SBiqd9TJen?usp=drive_link

I have updated this folder to include all of the necessary pre-processing files, in addition to the .nrrd file.

[amymmorton]

John, Suggestions: Scene folder : Knee_Sample_CT.nrrd (So that a user could replicate your PV, .. could you either save the sementations (if segmented in Slicer) in the Scene folder) Or include stl Models?

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On Mon, Feb 3, 2025 at 11:04 AM John Holtgrewe ***@***.***> wrote: @sbelsk <https://github.com/sbelsk> https://drive.google.com/drive/folders/14LtstqHeILYnRdkVMqYdN7SBiqd9TJen?usp=drive_link I have updated this folder to include all of the necessary pre-processing files, in addition to the .nrrd file. — Reply to this email directly, view it on GitHub <#138 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUUPFU4XO7WSPK67PMHUDT2N6HRTAVCNFSM6AAAAABRFCUTLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZRGQZDKMBYGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- ----------- Amy Morton MSc *Senior Research Engineer - Software* *Brown University Healt**h* Orthopaedic Research, 1 Hoppin Street, Coro West, 4th Providence, RI 02903-4923 linkedin <https://www.linkedin.com/in/amy-morton-35374340/>

[jdholt04]

That's a good idea. I added a Scene folder with the segmentation file from Slicer.

[amymmorton]

perhaps also include a readme.md file of processing?

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On Mon, Feb 3, 2025 at 11:38 AM John Holtgrewe ***@***.***> wrote: That's a good idea. I added a Scene folder with the segmentation file from Slicer. — Reply to this email directly, view it on GitHub <#138 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUUPFRDKPJO44H77I7ZGPD2N6LORAVCNFSM6AAAAABRFCUTLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZRGUYDSNBSHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- ----------- Amy Morton MSc *Senior Research Engineer - Software* *Brown University Healt**h* Orthopaedic Research, 1 Hoppin Street, Coro West, 4th Providence, RI 02903-4923 linkedin <https://www.linkedin.com/in/amy-morton-35374340/>

[amymmorton]

@sbelsk finalized updates to Wrist sample data