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update prostate lesion #398

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update prostate lesion
jtetrea Oct 1, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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108 changes: 54 additions & 54 deletions prostate-mri-lesion-seg/LICENSE
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Prostate-MRI_Lesion_Detection, v2.0 (Release date: August 2, 2023)
• DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH

• PROVIDER: the National Cancer Institute (NCI), a participating institute of the
National Institutes of Health (NIH), and an agency of the United States Government.

• SOFTWARE: the machine readable, binary, object code form,
and the related documentation for the modules of the Prostate-MRI_Lesion_Detection, v2.0
software package, which is a collection of operators which accept (T2, ADC, and High
b-value DICOM images) and produce prostate organ and lesion segmentation files

• RECIPIENT: the party that downloads the software.

By downloading or otherwise receiving the SOFTWARE, RECIPIENT may
use and/or redistribute the SOFTWARE, with or without modification,
subject to RECIPIENT’s agreement to the following terms:

1. THE SOFTWARE SHALL NOT BE USED IN THE TREATMENT OR DIAGNOSIS
OF HUMAN SUBJECTS. RECIPIENT is responsible for
compliance with all laws and regulations applicable to the use
of the SOFTWARE.

2. THE SOFTWARE is distributed for NON-COMMERCIAL RESEARCH PURPOSES ONLY. RECIPIENT is
responsible for appropriate-use compliance.

3. RECIPIENT agrees to acknowledge PROVIDER’s contribution and
the name of the author of the SOFTWARE in all written publications
containing any data or information regarding or resulting from use
of the SOFTWARE.

4. THE SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
ARE DISCLAIMED. IN NO EVENT SHALL THE PROVIDER OR THE INDIVIDUAL DEVELOPERS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.

5. RECIPIENT agrees not to use any trademarks, service marks, trade names,
logos or product names of NVIDIA, NCI or NIH to endorse or promote products derived
from the SOFTWARE without specific, prior and written permission.

6. For sake of clarity, and not by way of limitation, RECIPIENT may add its
own copyright statement to its modifications or derivative works of the SOFTWARE
and may provide additional or different license terms and conditions in its
sublicenses of modifications or derivative works of the SOFTWARE provided that
RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
with the conditions stated in this Agreement. Whenever Recipient distributes or
redistributes the SOFTWARE, a copy of this Agreement must be included with
each copy of the SOFTWARE.
Prostate-MRI_Lesion_Detection, v3.0 (Release date: September 17, 2024)
DEFINITIONS: AUTHOR(S) NVIDIA Corp. and National Cancer Institute, NIH
PROVIDER: the National Cancer Institute (NCI), a participating institute of the
National Institutes of Health (NIH), and an agency of the United States Government.
SOFTWARE: the machine readable, binary, object code form,
and the related documentation for the modules of the Prostate-MRI_Lesion_Detection, v2.0
software package, which is a collection of operators which accept (T2, ADC, and High
b-value DICOM images) and produce prostate organ and lesion segmentation files
RECIPIENT: the party that downloads the software.
By downloading or otherwise receiving the SOFTWARE, RECIPIENT may
use and/or redistribute the SOFTWARE, with or without modification,
subject to RECIPIENT’s agreement to the following terms:
1. THE SOFTWARE SHALL NOT BE USED IN THE TREATMENT OR DIAGNOSIS
OF HUMAN SUBJECTS. RECIPIENT is responsible for
compliance with all laws and regulations applicable to the use
of the SOFTWARE.
2. THE SOFTWARE is distributed for NON-COMMERCIAL RESEARCH PURPOSES ONLY. RECIPIENT is
responsible for appropriate-use compliance.
3. RECIPIENT agrees to acknowledge PROVIDER’s contribution and
the name of the author of the SOFTWARE in all written publications
containing any data or information regarding or resulting from use
of the SOFTWARE.
4. THE SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
ARE DISCLAIMED. IN NO EVENT SHALL THE PROVIDER OR THE INDIVIDUAL DEVELOPERS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.
5. RECIPIENT agrees not to use any trademarks, service marks, trade names,
logos or product names of NVIDIA, NCI or NIH to endorse or promote products derived
from the SOFTWARE without specific, prior and written permission.
6. For sake of clarity, and not by way of limitation, RECIPIENT may add its
own copyright statement to its modifications or derivative works of the SOFTWARE
and may provide additional or different license terms and conditions in its
sublicenses of modifications or derivative works of the SOFTWARE provided that
RECIPIENT’s use, reproduction, and distribution of the SOFTWARE otherwise complies
with the conditions stated in this Agreement. Whenever Recipient distributes or
redistributes the SOFTWARE, a copy of this Agreement must be included with
each copy of the SOFTWARE.
12 changes: 6 additions & 6 deletions prostate-mri-lesion-seg/README.md
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# Prostate MRI Lesion Segmentation - MONAI Deploy MAP

<p float="left">
<img src="imgs/organ_seg.png" width="200" />
<img src="imgs/lesion_prob.png" width="200" />
<img src="imgs/lesion_mask.png" width="200" />
<img src="imgs/organ_seg.png" width="300" />
<img src="imgs/lesion_prob.png" width="300" />
<img src="imgs/lesion_mask.png" width="300" />
</p>

This workflow takes T2, ADC, and HighB MRI series as input and produces several NIfTI files as output. These outputs contain organ and lesion segmentations and lesion probability maps.

## Software and Setup

In order to run this workflow and build a MAP you will need to [install MONAI Deploy App SDK](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/getting_started/installing_app_sdk.html). The workflow is currently verified against version 0.5.1. On most systems this can be easily done with the command `pip install monai-deploy-app-sdk==0.5.1`.
In order to run this workflow and build a MAP you will need to [install MONAI Deploy App SDK](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/getting_started/installing_app_sdk.html). The workflow is currently verified against version 2.0.0. On most systems this can be easily done with the command `pip install monai-deploy-app-sdk==2.0.0`.

It is also recommended to have an NVIDIA GPU with at least 12 GB of memory available.

## Using this Repository

The easiest way to get started with this workflow is to run on a test image taken from the [ProstateX](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=23691656) dataset. The `tutorial.ipynb` file walks through this process using ProstateX-0004 which can be [downloaded separately](https://drive.google.com/drive/folders/17oOgs1jIgJUxtkBRLATUdNrLSNQCLpCn?usp=drive_link) and placed in a `test-data/` directory.
The easiest way to get started with this workflow is to run on a test image taken from the [ProstateX](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=23691656) dataset. The `build_and_run.ipynb` file walks through this process using ProstateX-0004 which can be [downloaded separately](https://drive.google.com/drive/folders/1besSncSLlbeiv7UWveRJoOYQXOzu3JkU?usp=sharing) and placed in a `test-data/` directory.

After validating on test data, you can test this image on your own study or dataset. One of the main considerations when adapting to a new dataset will be the making sure the [DICOM Series Selector Operator](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/modules/_autosummary/monai.deploy.operators.DICOMSeriesSelectorOperator.html#monai.deploy.operators.DICOMSeriesSelectorOperator) is configured to properly differentiate between the different naming schemes and properties of the new dataset.

Expand All @@ -28,7 +28,7 @@ There are also scripts in the `scripts/` directory that test the workflow locall

## Models

The models needed to build and execute the pipeline (1 organ segmentation model, 5 lesion segmentation models) are hosted separately on [Google Drive here](https://drive.google.com/drive/folders/1wO4h5AON0MA3dxwnzl9cJlxjPxsfXcCF?usp=sharing).
The models needed to build and execute the pipeline (1 organ segmentation model, 5 lesion segmentation models, 1 classification model) are hosted separately on [Google Drive here](https://drive.google.com/drive/folders/1EpjrlzEdV7CcaCYqGTIEzOapamP4Ag6M?usp=sharing).

Download these models and put them inside a folder named `prostate_mri_lesion_seg_app/models` alongside the rest of the application code. Pipeline creation and execution will not complete if the model file path is changed or renamed.

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