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Imports overview tables

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michaelkain edited this page Mar 10, 2023 · 41 revisions

Import formats:

1. DICOM (pseudonymised or not)

Modality: MR (Original MR + Enhanced MR)

Additionally to standard MR images, in DICOMs:

  1. MR Spectroscopy (MRS): see MRS
  2. Physiological Data (_PhysioLog): see PD
  3. Diffusion Tensor Imaging (DTI): see DTI
  4. _RGB Secondary Captures (without PHI)

Modality: CT (Original CT + Enhanced CT)

Modality: PT (Original PT + Enhanced PT)

The current DICOM import (zip+pacs) ignores DICOM series, that have non-imaging modalities, like structured reporting (SR) or others. The allowed modalities are referenced here: AcquisitionModality.java. Furthermore series without DICOM instances are ignored too.

Pseudonymised DICOM files

Shanoir-NG applies during all imports itself a pseudonymization to all DICOM files, depending on different pseudonymization profiles. Shanoir-NG has successfully be used within multiple studies with previously pseudonymised DICOM files too, where users uploaded DICOM files, they pseudonymised on their own before the upload. In general the import works with these files, as it completes or searches as good as possible to allow an import. In any case, Shanoir-NG applies its own pseudonymization routine during the import to assure the same quality of pseudonymization for all data. Depending on the big variety of tools, that could be used by users before to perform a pseudonymization on their own before starting the import into Shanoir, there might be cases, where the import fails, because of a too hard removal of vital data for the data structure in Shanoir-NG.

More details:

  • If the patientBirthDate is completely removed by pre-pseudonymization: 19000101 is used instead to assure an import.

2. Bruker (Micro MR), Preclinical Extension

Dicomifier is used to convert from Bruker to DICOM, and after a standard MR DICOM import is performed, that allows to complete preclinical informations on the subjects and the examinations.

Specific fields for preclinical examinations:

  1. Anesthetic (type, injection interval, injection site, injection type, Dose)
  2. Physiological data: associated file (Heart rate, respiratory rate, SaO2, temperature)
  3. Blood gas data: associated file These files can be downloaded

Specific fields for preclinical subjects:

  1. Specy
  2. Strain
  3. Biological type
  4. Provider
  5. Stabulation
  6. Pathologies (Type of pathology, location and dates)
  7. Therapies (type of therapy, dose, molecule and dates)

This information has to be set manually during the import.

3. EEG: European Data Format (.edf) and BrainVision (.vhdr, .vmrk, .eeg)

The data is processed following its extension. Channels are parsed to be displayed. There is no visual data associated.

4. Brain Imaging Data Structure (BIDS)

  1. NIfTI (raw, just converted), single-subject ZIP file via WebGUI

We do NOT import the /sourcedata and not import the /derivates folder, but the raw NIfTI file structure.

5. Processed Datasets:

  1. NIfTI (1. + 2.)
  2. Analyze
  3. BIDS Derivatives (upcoming, not yet)

6. "Unprocessed" Files:

  1. Extra Data Files (-> Exam): any
  • Spectroscopy: rda for Siemens, spar+sdat for Philips
  • Task Logs (for functional MR)
  • Physiological Logging (not _PhysioLog, examples: .RESP, .ecg, .puls recorder via ideacmdtool menu for Siemens)
  1. Study Protocol File: .pdf
  2. Data User Agreement (DUA): .pdf

Import types

No. Format Type Modality DICOM IOD Microservices
1. DICOM PACS, ZIP, ShUp MR, CT, PT MRI, CTI, PTI, MRIE, CTIE, PTIE Import -> Dataset
2. Bruker ZIP MR MRI (as converted to DICOM) Import -> Dataset
3.1 NIfTI ZIP BIDS MR, CT, PT (none, as not DICOM) Import -> Dataset
3.2 NIfTI Processed Dataset MR, CT, PT (none, as not DICOM) Import (upload) + Dataset via front
4 EEG ZIP EDV or BV EEG (none, as not DICOM) Import -> Dataset
  • MRI == MR Image
  • MRIE == MR Image Enhanced
  • CTI == CT Image
  • CTIE == CT Image Enhanced
  • PTI == PT Image
  • PTIE == PT Image Enhanced

Import scenarios

No. Tool Type Format Input Comment
1. Web GUI (Angular) From file DICOM Upload: ZIP with DICOMDIR
2. Web GUI (Angular) From file DICOM Upload: ZIP with DICOM files, no DICOMDIR
3. Web GUI (Angular) From file DICOM Upload: ZIP with multiple exams DICOM
4. Web GUI (Angular) From PACS DICOM DICOM Q/R to PACS: PACS<->ShServer c-move activated
5. ShanoirUploader From file DICOM Directory with DICOMDIR
6. ShanoirUploader From file DICOM Directory with DICOM files, no DICOMDIR
7. ShanoirUploader From PACS DICOM DICOM Q/R to PACS: PACS<->ShUp<->ShServer c-move activated
8. Web GUI (Angular) From Bruker Bruker Upload: ZIP with Bruker format small animal
9. Web GUI (Angular) From EEG EDF Upload: ZIP with EDF format EEG as .edf file
10. Web GUI (Angular) From EEG VHDR Upload: ZIP with Brainvision format EEG as vhdr file
11. Web GUI (Angular) From BIDS NIfTI Upload: ZIP with BIDS (one subject) Brain Imaging Data Structure
12. Web GUI (Angular) From Processed Dataset NIfTI Upload: NIfTI file
13. ShanoirUploader From PACS DICOM CSV file MASS IMPORT with DICOM Q/R to PACS: PACS<->ShUp<->ShServer c-move activated

PACS<->ShServer: a direct network connection needs to exist between the PACS and the Shanoir server.

The Bruker file import is a special case of the DICOM import, where a Bruker ZIP file is uploaded and converted into DICOM format. After the conversion the import is a normal 1. import.

Multiple examinations import

It is possible to import multiple examinations for one subject in shanoir. This is possible by checking the checkbox at the beginning of the DICOM import.

The archive has to be structures as follow: image

Examinations and subject are automatically created, using data from the dicom in itself. The fields to select are:

  • Study in which we import the data
  • Default study card that will be used during the import.
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