search

lab-midas / TCIA_processing

autoPET TCIA pipeline
MIT License
34 stars 11 forks source link

Question about fused FDG-PET/CT dataset #2

Open yrsunn opened 7 months ago

yrsunn commented 7 months ago

Hey, I have two questions:

Thanks for your time!

thomaskuestner commented 7 months ago
  1. Most DICOM viewers let you create these kinds of images as overlay of PET or CT (in their respective color maps) with the masks. For example 3D Slicer or MITK can provide you this image. We have no code in this repository to create this image output.
  2. Please refer to the "clinical data" csv file on TCIA: https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=93258287 "NEGATIVE" refers to patients with no FDG-avid lesion uptake = "healthy" Please note that they are not actually healthy, as they had some primary indication to receive a PET/CT imaging.
DanguiYang commented 5 months ago

微信截图_20240115225402 Hey, I have one questions: Why is there no response and no output after I input according to the format conversion command?

thomaskuestner commented 5 months ago

tcia_dicom_to_mha.py seems to be a file which you created yourself? We don't have this in the repository, hence I cannot tell you why this is not working. python3 tcia_dicom_to_nifti.py F:/manifest-...../DICOM/FDG-PET-CT-Lesions/ F:/maniftest-..../NIFTI/FDG-PET-CT-Lesions/ should work

DanguiYang commented 5 months ago

tcia_dicom_to_mha.py seems to be a file which you created yourself? We don't have this in the repository, hence I cannot tell you why this is not working. python3 tcia_dicom_to_nifti.py F:/manifest-...../DICOM/FDG-PET-CT-Lesions/ F:/maniftest-..../NIFTI/FDG-PET-CT-Lesions/ should work

联想截图_20240116101342 联想截图_20240116101403 Sorry, my screenshot is wrong, I tried the command you gave, and it still doesn't work, this is the file directory where I downloaded the data, I don't know if there is a problem with the file directory I entered

thomaskuestner commented 5 months ago

Do you have read/write access in these directories? For us this is all working and since you do not see any error message, I assume that there is nothing wrong with the code. Can you debug yourself through the code and see if it branches out of the code before creating any files?