Need Help in conversion to TVB format

[Pallab K]

  Hi,

I intend to use Parkinson's Progression Markers Initiative (PPMI) Data in TVB which have files in the three different imaging modalities (Anatomical, DTI, fMRI).

I am getting stuck while uploading the input files in the server as I am unable to do the run 'tvb_pipeline_v1.1_encryption.ipynb' for encrypting and putting the files in the cluster.

Also, the 'Pipeline Video Tutorial' given in the 'https://wiki.ebrains.eu/bin/view/Collabs/tvb-pipeline/' is outdated and shows another script.

Can someone help me in changing my data into TVB format ?

Data Link : https://drive.google.com/file/d/19F2ADiCelEoLfULD3bjJkxWJ4zegXmKp/view?usp=sharing

Regards,

Pallab

[Michael Schirner]

Hi Pallab,

can you describe the problem that you encounter? Please note that for running the pipeline an account with one of the backend supercomputers is needed.

I would like to suggest to remove public access to the patient data that was shared in the original post. For EU citizens sharing this data with an indefinite number of people and without an established lawful basis for each individual case would violate the EU's data protection regulation GDPR (for example, Articles 9 and 25: gdpr-info.eu).

Best,
Micha

[Pallab K]

Hi Micha,

  

I have been granted access to 'DAINT-CSCS' supercomputer through Ebrains Collaboratory. But, I am unable to execute the code as it shows authentication error. Also, I am facing problems in AES encryption and uploading my data in the cluster. Would appreciate if someone could help me change my data to TVB format.

Also, I have removed all the subject private information from the data and also it is downloaded from an opensource database. Hope , in the pursuit of scientific excellence, the users would overlook the legalities and help me in my endeavour.

Regards,

Pallab

[Michael Schirner]

Hi Pallab,

can you send me the error message(s)?

Without knowing the concrete error, another problem that comes to mind is that your EBRAINS account must be mapped with your CSCS account. Was this done? It probably requires a support request with EBRAINS.

Note: MRI data contains health data that can be potentially identified and hence is classified special category of data as of GDPR. Removing primary indentifiying information is a protective measure but does not render the data to be anononymous not falling under GDPR protection. They remain special category of data and hence sharing without lawful basis for each individual case is not lawful. This is true also if data are downloaded from a public repository.

Best,
Micha

[Pallab K]

Hi Micha,

Thank you for your concern, I have removed the data from the link attached above. I would like you to kindly help me step-by-step in executing the TVB-pipeline script. Following are my concerns :

1. I have an EBRAINS account and when I go to 'Lab' in EBRAINS Collab, I get the following options:

After, selecting 'DAINT-CSCS', I run the script, then I get the following error:

How do I map my EBRAINS account to CSCS account?

Also, how do I encrypt my input files to AES encryption and how should I upload it? I haven't found any documentation for uploading.

Thanks and Regards,

Pallab

[Michael Schirner]

Hi Pallab,

the error message indicates that your accounts are not mapped (your role is "anonymous"). I would suggest to write to EBRAINS support (ebrains.eu/support) supplying your account names at EBRAINS and CSCS and asking to map your accounts. 

The documentation for encryption and uploading can be found further down in the notebook under the headings "Step 8. Encrypt input data" and "Step 9. Upload encrypted input data".

Best,

Micha