Using proper KCNI naming convention to label projects, participants, experiments, and files is extremely important as data is routed through the Neuroinformatics Platform according to these labels. Please take great case in ensuring data is properly labelled at every level, codes are consistent throughout the project life cycle and typos are avoided. Thank you!
Project ID
The project ID must be a 3 character project code, followed by a two digit study code, followed by an underscore and finally a 3 character site code.
Ex. ABC01_CMH
| Example | Definitition | Restrictions/Rules | Notes |
|---|---|---|---|
| ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
| 01 | Study Code | 2 Numerals | Typically '01', unless describing divisions within a project |
| CMH | Site Code | 3 Uppercase Letters | Must be chosen from site code list HERE |
A Project Code will be assigned when you meet with the Neuroinformatics Platform Admin at your initial project on-boarding meeting. If you already use a project code in some other capacity (including but not limited to NGDB or TIGR Lab XNAT), please share this at the meeting as it is best to keep the same project code across platforms/databases.
The Study Code is used to distinguish unique studies within a larger project, including sub-studies or study variations. Some big projects or labs will have multiple studies under the same project.
One or more Site Codes will be used based on the location(s) of the study. See the Standardized Site Codes table for a list of current study sites and their corresponding site codes.
Study Participant ID
It is important that each project Subject is assigned exactly 1 Subject ID that is unique across the project. In multi-site or multi-modality projects, care must be taken to ensure the same Subject is not assigned multiple Subject IDs at different sites or across different modalities. Of equal importance is the precise Subject ID entry at every data entry occurence. A Subject ID typo can have significant consequences throughtout the Neuroinformatics Platform system.
The Subject ID must be the concatenation of the Project ID, an underscore and a Subject Code.
Ex. ABC01_CMH_00000001
| Example | Definitition | Restrictions/Rules | Notes |
|---|---|---|---|
| ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
| 01 | Study Code | 2 Numerals | Typically '01', unless describing divisions within a project |
| CMH | Site Code | 3 Uppercase Letters | Must be chosen from the Site Code List |
| 00000001 | Subject Code | 4-8 Alphanumeric Characters | See Subject Code Guidelines |
The Subject Code denotes a specific person (or animal) within the study.
Guidelines for choosing an appropriate Subject Code:
- must be 4 to 8 characters long
- preferably contains only numeric digits, but can include uppercase letters if needed
- recomended to start at 00000001 and increment as necessary
- must not contain lowercase letters, symbols, or whitespace (spaces, tabs, etc)
- must not include PHI (e.g., diagnosis), case/control status, or other sensitive information
- must not contain the characters 'PHA' in positions 4-6, since these indicate "phantom" (non-human) images in XNAT
- must not contain any coding related to location, visit, or any other code that is not representative of the participant. (eg. BAD: ABC01_CMH_V10001 - where V1 represents the first visit)
If you have already started collecting data and your participants do not follow this naming convention, please indicate this at your Neuroinformatics Platform project on-boarding meeting as a name conversion script might need to be implemented.
Experiment Label
NOTE: It's important that the MRI or PET operator use the Experiment Label as the Patient Name in the DICOM header during an MRI or PET session.
Please ensure the Experiment Label is entered correctly at all data entry occurences as a misspelled Experiment Label can have significant consequences throughout the Neuroinformatics Platform system.
The Experiment Label must be the Study Participant ID concatenated with the visit code, session code and modality code using underscores.
Ex. ABC01_CMH_00000001_02_SE03_MR
| Example | Definitition | Restrictions/Rules | Notes |
|---|---|---|---|
| ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
| 01 | Study Code | 2 Digits | Typically '01', unless describing divisions within a project |
| CMH | Site Code | 3 Uppercase Letters | Must be chosen from the Site Code List |
| 00000001 | Participant Code | 4-8 Alphanumeric Characters | See Participant Code Guidelines |
| 02 | Visit Code | 2 Digits | Increment each visit |
| SE03 | Session Code | SE followed by 2 Digits | Incement each session within a visit |
| MR | Modality Code | 2-4 Uppercase Letters | Must be chosen from the Modality Code List |
The Visit Code is 2 integers that represent the visit number. For example, 01 is first baseline visit, 02 is a follow-up visit, etc..
The Session Code is the letters 'SE' followed by 2 integers which distinguish different data capture sessions in a single visit. For example, if you are conducting an MRI experiment and you collect data before some intervention, the participant leaves the scanner for the intervention, then the participant returns to the scanner the session code should be incremented by 1. Notice the difference between visit and session where a visit denotes a participant coming to the institution for data acquisition where a session is denoted as a continuous acquisition of scans.
The Modality Code is 2 to 4 characters, denoting the modality with which the data was acquired. See the list of image modality codes below. For example, MR = Magnetic Resonance Imaging which includes fMRI, MRI, MRS etc.
EEG Data Filename
When saving an EEG data file that is to uploaded by automated data upload processes in XNAT it is important to properly label the file to ensure the data can be organized into its proper XNAT storage location.
The data files should follow the Experiment Label convention followed by an underscore, then a trial code.
Ex. ABC01_CMH_00000001_02_SE03_EEG_rest.cnt
| Example | Definitition | Restrictions/Rules | Notes |
|---|---|---|---|
| ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
| 01 | Study Code | 2 Digits | Typically '01', unless describing divisions within a project |
| CMH | Site Code | 3 Uppercase Letters | Must be chosen from the Site Code List |
| 00000001 | Participant Code | 4-8 Alphanumeric Characters | See Participant Code Guidelines |
| 02 | Visit Code | 2 Digits | Increment each visit |
| SE03 | Session Code | SE followed by 2 Digits | Incement each session within a visit |
| EEG | Modality Code | 2-4 Uppercase Letters | Must be chosen from the Modality Code List |
| rest | Trial Code | 1+ Alphanumeric Characters | Used to describe the trial experiment |
The Trial code is usually used to describe different runs within a session. For example rest is common to describe continuous resting data. Other popular examples are single or lici for TMS trials and 1Back, 0Back, etc. for NBack trials.
Notes:
- DO NOT use commas, periods, underscores, spaces, dashes, slashes or other punctuation in the trial code. Instead use camel case (ex. thisIsACamelCaseExample)
- Ensure that the trial code is consistent across experiments and scans. For example, using 0Back, zeroBack or 0back will cause errors later on
Phantom Naming Convention
Phantom data is used in imaging studies to measure scanner variability over time. On the KCNI XNAT, phantom data must be labelled slightly differently compared to in-vivo data.
Phantom Participant Label
The Phantom Participant Label must be the concatenation of the Project Label and the combination of the phantom type with the phantom identifier joined by an underscore.
Ex. ABC01_CMH_LEGPHA
| Example | Definitition | Restrictions/Rules | Notes |
|---|---|---|---|
| ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
| 01 | Study Code | 2 Digits | Typically '01', unless describing divisions within a project |
| CMH | Site Code | 3 Uppercase Letters | Must be chosen from the Site Code List |
| LEG | Phantom Type Code | 3 Uppercase Letters | Must be chosen from Phantom Type List |
| PHA | Phantom Identifier Code | Always PHA |
The Phantom Type is a 3 character code that describes the construction of the phantom. This code must be chosen from the Phantom Types List below. Ex: LEG = Lego phantom
The Phantom Identifier is the letters 'PHA' that identifies the subject as a phantom
Phantom Experiment Label
The Phantom Experiment Label must be the Phantom Experiment Label concatenated with the session code and modality code using underscores.
Ex. ABC01_CMH_LEGPHA_200511_MR
| Example | Definitition | Restrictions/Rules | Notes |
|---|---|---|---|
| ABC | Project Code | 3 Uppercase Letters | Chosen in coordination with KCNI admin. Preferably a project acronym. Cannot match existing project. |
| 01 | Study Code | 2 Digits | Typically '01', unless describing divisions within a project |
| CMH | Site Code | 3 Uppercase Letters | Must be chosen from the Site Code List |
| LEG | Phantom Type Code | 3 Uppercase Letters | Must be chosen from Phantom Type List |
| PHA | Phantom Identifier Code | Always PHA | |
| 200511 | Date Code | 6 Digits | Date of data acquisition (YYMMDD) |
| MR | Modality Code | 2-4 Letters | Must be chosen from Modality Code List |
The Phantom Date code is 6 digits representing the date of your scan (ex. yymmdd).
The Modality code is the same as the human Modality code. It is a string of 2 to 4 characters which denotes the modality with which the data was captured.
Modality Codes
The Modality Code denotes the apparatus with which the imaging data was acquired and is appended to the end of the Experiment Label. Only Modality Codes chosen from the list below are considered acceptable. If you are collecting data that is not well described by one of the listed modalities, please contact XNAT Admin and your imaging modality can be added.
| Imaging Modality | Modality Code |
|---|---|
| Computed Radiography | CR |
| Computed Tomography | CT |
| Digital Radiography | DX |
| 3d Digital Radiography | DX3D |
| Electrocardiography | ECG |
| Electroencephalography | EEG |
| Electrophysiology | EPS |
| Visible Light Endoscopy | ES |
| Video Endoscopy | ESV |
| Visible Light Microscopy | GM |
| Video Microscopy | GMV |
| Hemodynamic | HD |
| Intraoral Radiography | IO |
| Magnetoencephalography | MEG |
| Digital Mammography | MG |
| Magnetic Resonance | MR |
| Nuclear Medicine Image | NM |
| Ophthalmic Photography | OP |
| Opthalmic Tomography | OPT |
| Positron Emission Tomography | PET |
| Radiofluoroscopy | RF |
| Radiotherapy | RT |
| Visible Light Slide-Coordinates Microscopy | SM |
| Ultrasound | US |
| X-ray Angiography | XA |
| X-ray 3d Angiography | XA3D |
| Visible Light Photography | XC |
| Video Photography | XCV |
Phantom Type Codes
Below is a list of acceptable Image Phantom Types. If you have a phantom that is not well described by one of the codes in this list, then please contact XNAT Admin and your phantom can be added.
| Description | Phantom Code |
|---|---|
| Lego Phantom | LEG |
| fBIRN Phantom | FBN |
| Hoffman Phantom | HOF |
| GE Phantom | GE |
| ADNI Magphan Phantom | ADN |
| ACR Phantom | ACR |