Data Naming

Who is this for?

• Anyone who will access the data stored in /archive
• Anyone who will help curate the data stored in /archive

This document describes a naming protocol for our data files that explicitly indicates who, what, when, and where the data was acquired. The naming protocol is inspired by the OBI naming scheme.

Data Naming Protocol

Standard Prefix

Generally, each data file should start with a string that follows this pattern:

[study]_[site]_[subjectid]_[timepoint]_[session]

Where,

• [study] is a short code indicating the overall study (eg. "DTI") and may be modified to indicate major study protocol differences (e.g. "COGBDY" vs. "COGBDO" to distinguish between young and older COGBD protocols).
• [site] indicates the site/scanner used (e.g. CMH indicates the CAMH 3T scanner)
• [timepoint] indicates which time point in the study design the data was collected for (e.g. 01 for baseline, 02 for 5yr follow up, etc..)
• [session] is a sequential numbering over scans at each time point in order that repeats/redos are obvious (i.e. the first scan at time point 01 is labeled _01_01, and a redo scan to collect a mis-acquired sequence would be labeled with as _01_02).

For example, the first time a follow up scan for subject H240 is completed in the "DTI" study using the CAMH scanner, we might label it as DTI_CMH_H240_02_01. If the subject had to come in a second day to complete or repeat some acquisitions, we would label those files as DTI_CMH_H240_02_02 (i.e. a session code of '02' because this is the second time they've come in for the '02' timepoint).

The following table lists our current studies by name, study and site codes to use in the naming, and a few example file names to illustrate this naming protocol in action:

Study Name	Study Code	Sites	Examples
Anorexa study	ANDT	CMH	ANDT_CMH_201_01_01
Autism study	ASDD	CMH	ASDD_CMH_EF00_01_01
DTI study	DTI	TGH, CMH	DTI_TGH_H001_01_01
SPINS	SPN01	CMH, ZHH, MRC	SPN01_CMH_0002_01_02
COGBD older	COGBDO	CMH	COGBDO_CMH_203211_01_01
COGBD younger	COGBDY	CMH	COGBDY_CMH_208260_01_01
rTMS working mem	RTMSWM	CMH	RMTSWM_CMH_WM001_02_01
STOPPDII	STOPPD	MAS, PMC, NKI, CMH	STOPPD_PMC_310010_02_01
PRELAPSE	PRE01	many :D

Sites

Site	Code
Toronto General Hospital	TGH
Centre for Addiction and Mental Health	CMH
University of Massachusetts	MAS
Maryland Psychiatric Research Centre	MRC
Zucker Hillside Hospital	ZHH
Pittsburg Medical Center	PMC
Nathan Kline Institute	NKI
U Iowa College of Med	IWA
U Minnesota	MIN
Grady Hospital	GRD
Cherry Street	CRY
Borgess WMU School of Medicine	BRG
Creighton U.	CTN
Peace Health	PCE
Stanford University	SFD
U Texas	TXS
U Michigan	MCH

Naming Scans Within Exams

The naming scheme above specifies naming an entire dataset acquired at a point in time, but the naming scheme can be extended to label different kinds of data within that acquisition. For instance, in an MR exam, each series could be labelled separately to indicate T1 vs. T2 vs. DTI data.

Generally, extending naming should follow this convention:

<prefix>_[tag]_[series]_[description]

where

• <prefix> is the full prefix as described above.
• [tag] is a friendly short code to indicate the type of data, e.g. T1, T2, DTI33-1000
• [series] is a number enumerating this acquisition within the exam.
• [description] is longer and more specific string that describes the data. It should not contain underscores (_) or spaces. For instance, for exam series, the description field should be mangled (see below) version of the MR scanner's series description field, e.g. AXIAL-DIFFUSION-TENSOR-23

For instance, for the exam DTI_TGH_H001_02_01, we would have the following extended file names:

Series Description	Full Name
3-PLANE LOC	DTI_TGH_H001_02_01_LOC_01_3-PLANE-LOC
Calibration	DTI_TGH_H001_02_01__CAL_04_Calibration
AXIAL 3D SPGR IR PREP	DTI_TGH_H001_02_01_T1_04_AXIAL-3D-SPGR-IR-PREP
AX FSE PD/T2 2.0 mm	DTI_TGH_H001_02_01_PD_09_AX-FSE-PD-T2-2.0-mm
AX FLAIR	DTI_TGH_H001_02_01_FLAIR_12_AX-FLAIR
AXIAL DIFFUSION TENSOR (23)	DTI_TGH_H001_02_01_DTI23-1000_10_AXIAL-DIFFUSION-TENSOR-23
AXIAL DIFFUSION TENSOR (23)	DTI_TGH_H001_02_01_DTI23-1000_04_AXIAL-DIFFUSION-TENSOR-23
AXIAL DIFFUSION TENSOR (23)	DTI_TGH_H001_02_01_DTI23-1000_05_AXIAL-DIFFUSION-TENSOR-23

Mangling is simply this: characters that aren't numbers or letters are converted to a - character, and runs of -s are converted to a single -.

Study Naming

The protocol above outlines how data files should be unambiguously named after participants and sites are given identifiers. This section describes how, for our specific studies, we will generate new identifiers.

DTI Study

Subject identifiers follow the format:

diagnosis code (H or S) + four digit number

For example, H003 or S080. H = healthy control, S = schizophrenia. Historically there a few variations on this theme when the identifiers are written down:

1. Identifiers may start with 06, e.g. 06H003 or 06S080.
2. Identifiers may end with _2 to indicate a follow up scan. E.g. H003_2 or even 06H008_2.

Nevertheless, ongoing, when we refer to a DTI subject identifier, we mean the four character code version (e.g. 'H003', 'S080', ...).

Study protocol changes, and interaction with the SPINS study

The DTI study has undergone several changes in protocol (TODO: ref study protocol documents). However, essentially there have been two phases, pre-SPINS and post-SPINS. In the pre-SPINS phase, all participants were given IDs as described above, and scanned at TGH and CAMH sites. Once the SPINS study started, all participants under 51 are also participants of SPINS, and so are given both a DTI and a SPINS identifier (and, they are acquired at CAMH under the MR unit study code SPIN1MR). Participants 51 and older are only part of the DTI study (and, acquired using the CAMH DTI3MR study code).

Participants that have had an baseline scan pre-SPINS (and so only have a DTI identifier) but then return for a follow-up scan are treated as described above (i.e. given a baseline SPINS identifier if they are under 51 years old, but also given a DTI identifier).

Here's a table with some examples illustrating the above:

Age	Subj	Scan Type	SPINS ID	DTI ID
46	H240	Baseline	SPN01_CMH_H240_01_01	DTI_CMH_H240_01_01
51	H240	Followup	n/a	DTI_CMH_H240_02_01
40	H107	Baseline (pre-SPINS)	n/a	DTI_CMH_H107_01_01
45	H107	Followup (SPINS)	SPN01_CMH_H107_01_01	DTI_CMH_H107_02_01