BIAC's Processing Pipeline is a software system designed to automatically transfer data off of the scanner, run a series of automated processes on the dataset, and transfer the processed results to a directory where the user can get to it. This process depends on proper assignation of the dataset to a valid Experiment. Once assigned, data is processed according to Experiment based preferences, and the results are transferred to the appropriate Experiment directory, where users who have data access privileges can get to it.
Automated Imaging Management System ( AIMS ) is a multi-threaded python daemon that runs on a desktop connected to the internal GE switch. AIMS connects to the scanner console with sshfs to monitor the hard-drive for raw k-space data and adds new files to a copy queue thread to remove them from the scanner to reconstruct and archive. AIMS launches as dicom receiver to receive automated dicom pushes from the console. Once received there is a thread monitoring the receive location for new data to schedule processing and archive. During the processing of reconstructed or dicom data images are wrapped with with BXH headers, converted to nii.gz, and copied to individual experiment storage locations. If appropriate a full BIRN QA is run for functional data, which is uploaded to our webserver as well as copied to the experiment storage location. GE physio files are also transferred if they were collected. Imaging metadata and QA numbers are added to our imaging database for use with various web services.
A nightly cron job copies locally processed and raw data from the AIMS computers to a network attached storage location. This includes all k-space data, pfile headers, nii.gz data, physio files, etc.
On a monthly basis the archives are moved to a cloud based S3 cold storage location hosted by Duke.
For imaging data, the PatientID and ExperimentID that is entered on the scanner console is primarily used for identification. Our software takes what is entered in on the console, strips out the punctuation, and lowercases all text before before comparing against a list of valid Experiments.
If the ExperimentID entered on the scanner does not match a list of valid Experiments, or that Experiment's storage location is full, then our processing daemon will temporarily transfer data to our Salvage.01 experiment location. You can file a trouble ticket to get assistance receiving the salvage data.
You can look at our status monitor page and select Exams → Exam Number under the appropriate scanner which will display which series have been processed. Also you can check your experiment location on the BIAC 'Exam Tracker' page to see similar information and various QA measures.
If the error you see is 'Experiment Not Found', please submit a trouble ticket so our data administrators can know where the data was supposed to be sent. Our data admins will respond as soon as possible to the trouble ticket.
Looking for the Pipeline/Data Administration FAQ? Restricted. Request access by sending an email to Josh or Chris.