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From XNAT to BIDS

XNAT

RAW DICOMs from the scanner are stored on XNAT (xnat.nencki.edu.pl). You will receive your personal username and password once you register on the website.

DICOM to BIDS

We provide an easy-to-use tool that directly accesses XNAT to retrieve data - XNAT-DCM2BIDS, downloads it to your computer, and converts it to the BIDS structure. You will need your XNAT credentials to start the download, as well as a config.json file specifying the BIDS structure mapping. The configuration file is available on our GitHub repository:
https://github.com/nencki-lobi/lobi-mri-scripts/blob/main/dcm2bids/

Experiment logs and physiological recordings

Logs from experiments (Presentations) and additional recordings such as described below are available online through our cloud service.

We offer pulsoximetry (PPG) and respiratory (RESP) recording services for FMRI sessions, if required. To utilize these services, you will need to use the non-vendor EPI sequence from CMRR Minnesota, as it is the only sequence that allows for automatic saving of the respective files onto the disk. Although we do not provide analysis support for these files, you can refer to the instructions available on the CMRR GitHub website for guidance.

Anonymize DICOM tags

We consider our data anonymous, in a sense, that they do not contain textual information about the subjects (name, date if birth etc.). You may need to additionally modify codes or other fields of Your DICOM files before You share them.

All clones of Osirix (Horos/Miele) enable DICOM anonymization of specified tags eg. PatientID, Date of Birth etc. Click on Anonymize.. (on the bar or File-Anonymize) and select tags to be wiped out (Reset) or replaced with a custom text.

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