I am trying to run the liver segmentation workflow from Readme.pdf doc. My understanding of this workflow is when we provide DICOM series of abdominal images, the segmentation model by Nvidia clara helps us by segmenting the liver portion from the abdomen.
Am I right to understand that input will be a series of DICOM images (all associated) of abdomen?
Usually humans load it in a viewer and explore the image in different orientation to mark the region of interest? I believe this is done using dense networks. Am I right? And I can access the details of each container through the Table (port address) provided in doc. Is my understanding right? localhost:50051 should show me details about DICOM writer. I guess that’s the use of table section
Where are the input and output files stored? I know that we have test-data folder where there are images for abdominal study…Where is this path configured for the job to pick up the data? I don’t see any path info in “values.yaml” file and where is output image stored? Under clara-io folder, I only see the payload id (the id starts with 0000…) and corresponding input files for dicom-reader,writer etc but I don’t see anything in the “output” folder of dicom-writer whereas I see an .mhd and .raw files in the “input” folder of the dicom-writer. Absence of data under “OUTPUT” of dicom-writer is the reason for being not able to view the output? Can you let me know how this can be fixed?
How can I view the output - Organ marked as Liver? When I opened Clara Dashboard, there were no jobs, no rendered output even though I successfully executed the Clara-wf command as shown below. In AIAA, we had connection between MITK Client and AIAA server, so we were able to see.
I am following the guide steps and not sure whether I am missing any prerequisite here. For exploring reference/sample workflow, should I be doing anything by following chapter 6 (Clara containers) or just sticking to chapter 5 (Workflow Development Guide) should be suffice to see end-end workflow?
Please refer the attachment for the output that I got. Can you help me understand whether there is any issue with it? I was able to see that Startup, prepare,execute and cleanup was successful
./clara-wf test fd3ee8bf-b9f3-4808-bd60-243f870ff9bd
Your response would definitely help me gain a better understanding. Thank you