Closed Riksi closed 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.
Hi, any updates on this? Thanks.
The following newly available dataset might be useful to anyone interested in this issue. It consists of annotations for nodules >= 3mm in DICOM format.
The pylidc library is also really helpful for preprocessing.
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!
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$
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.