MIC-DKFZ / medicaldetectiontoolkit

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

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Using the LIDC dataset #2

Closed Riksi closed 5 years ago

Riksi commented 5 years ago

It looks like you have done some additional preprocessing on the LIDC dataset prior to running preprocessing.py, such as saving the data to a different format from the original DICOM files and making a csv file, characteristics.csv, with metadata in the xml files. Would you be able to share the code used on the raw data as downloaded from the source (https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI)? Thanks.

pfjaeger commented 5 years ago

thanks for reaching out. The preprocessing was done by a colleague who is not part of the project. I will ask him whether we can share the code and get back to you asap.

Riksi commented 5 years ago

Hi, any updates on this? Thanks.

Riksi commented 5 years ago

The following newly available dataset might be useful to anyone interested in this issue. It consists of annotations for nodules >= 3mm in DICOM format.

https://wiki.cancerimagingarchive.net/display/DOI/Standardized+representation+of+the+TCIA+LIDC-IDRI+annotations+using+DICOM

The pylidc library is also really helpful for preprocessing.

pfjaeger commented 5 years ago

Good news: thanks to my colleague Michel Goetz the data convention tools are now available at https://github.com/MIC-DKFZ/LIDC-IDRI-processing/tree/v1.0.1 Sorry for the wait guys!

shanpriya3 commented 5 years ago

22 I am trying to preprocess the LIDC dataset but I am getting the following errors. Can anyone help me with this?

No DICOM's found for file: /LIDC-IDRI-Preprocessing/LIDC_Dataset/XML_Data/LIDC-XML-only/tcia-lidc-xml/186/075.xml /LIDC-IDRI-Preprocessing/LIDC_Dataset/XML_Data/LIDC-XML-only/tcia-lidc-xml/186/049.xml /LIDC-IDRI-Preprocessing/LIDC_Dataset/XML_Data/LIDC-XML-only/tcia-lidc-xml/186/049.xml 1.3.6.1.4.1.14519.5.2.1.6279.6001.212697393127299815450339637649 1.3.6.1.4.1.14519.5.2.1.6279.6001.410251741986998833890312367579 [] No DICOM's found for file: /LIDC-IDRI-Preprocessing/LIDC_Dataset/XML_Data/LIDC-XML-only/tcia-lidc-xml/186/049.xml (CMAKE_QT) dv00:/LIDC-IDRI-Preprocessing/LIDC-IDRI-processing$