Running EBRAINS MRI Pipeline on remote supercomputer

[Eesha Bharti]

Hello! I am wondering how to run the EBRAINS MRI pipeline on my institution's supercomputer rather than uploading data to EBRAINS. Furthermore, my data isn't in BIDS format and I don't have the raw DICOM files in order to put the data into BIDS format – can I still run the TVB MRI preprocessing pipeline outlined on EBRAINS? 

Given these limitations, I've been trying to go through the pipeline outlined in the supplementary figure of this paper (https://www.sciencedirect.com/science/article/pii/S1053811915002505?via%3Dihub#ec0020) but have been getting stuck to no avail.

Thanks in advance!

Eesha

[Michael Schirner (michael.schirner@bih-charite.de)]

Hi Eesha,

yes, the three container images (1, 2, 3) can be run independently of EBRAINS on any computer with Docker or a similar container runtime. 

Regarding your second question, DICOM files are not strictly required to obtain a BIDS-compliant data set, it is well possible to start from NIFTIs. 

Yes, it's easy to get stuck with such complex pipelines. What helped me was to go as an initial learning experience manually through each individual pipeline step, comparing inputs with outputs, checking the plausibility of the applied transformations, etc. This process is usually required for quality control in any case, since MRI pipeline steps are often based on heuristics that can easily fail.

Best,

Michael