Nick Knouf <nknouf@mit.edu> 2003-12-01 First stab at a fMRI ontology. http://visus.mit.edu/fontomri/0.01/fontomri.owl fMRI, ontology, fMRI analysis, foo, bar fontomri: An Ontology to describe fMRI experiments Possible ontology to describe everything about fMRI experiments. Aborted scan session, due to equipment malfunction. The set of all aborted scan sessions. Aborted scan session, due to the subject. asldkjjfas;ldfkjasdf Any thing (living or non-living, single or a group, independent or institutional) that is capable of an action on its own, and said action impacts a study or study analysis. The set of classes and properties that define a particular analysis. The generic class of anatomic runs. Anatomical runs can include MPRAGE, T1 weighted EPI images, and so on. A computer used for behavioral experiments, or stimulus presentation, or both. The generic class of diffusion runs. EEG Devices Any equipment used in a study. An experiment. At this time it is not clear if this might go over multiple sessions; it could, if perhaps you scan one subject on a portion of runs one day and have them return the next week for the rest of the runs in order to make the scan sessions a managable length of time. An experimental session; in many cases this will be identical to the experiment class, but this distinction is important in some cases. face duration experiments performed by Foo Bar all experiments that have something to do with face orientation. The larger class of face recognition experiments. XX Female The generic class of functional runs. I/O makeup session; this is time that we are not usually assigned, but we use as makeup for lost fmri:NormalSession(s). I/O session; this is time that we are not usually assigned and is thus charged at twice the normal rate. Lab policy is to not use I/O time unless urgently needed. The set of all I/O scan sessions. Institutional Review Board (IRB). An example of a non-human agent that is involved in fMRI research. Magnetoencephalography (MEG) scanners. MRI coils used in research. The manufacturer of a scanner used in a study or experiment. Examples include Siemens or GE. The model name of a scanner used in a study or experiment. For example, with Siemens scanners, model names include Trio, Allegra, and Sonata. An individual MRI run; can be functional, anatomical, diffusion, etc. MRI Scanners XY Male Normal session, charged at the reduced rate. Unless otherwise noted, all fmri:ExperimentSession(s) are fmri:NormalSession(s). A human-being involved in fMRI research. David Brainard, Denis Pelli and Allen Ingling http://psychtoolbox.org Psychophysics Toolbox is a set of Matlab scripts and MEX files for presentation of stimuli on pre-Mac OS X systems (or in OS X through Classic, although timing may be an issue). A researcher in an experiment. May also be a _Subject_. A particular scanner protocol; in the case of MGH scanners, this might be "ge_functionals". Type of experimental session; for example, we can use this to indicate that a session was the 'normal' type (and thus charged at the usual rate) or an 'I/O' slot (and thus charged at twice the normal rate). chromosomal sex Software used for stimulus presentation. A combination of experiments and subjects that describes a larger research plan. Name of a Study The general type of a study; useful for connecting IRB approvals to particular studies. A subject in an experiment. May also be a _Researcher_. 3.0 30 full 5.0 The date of the subject's birth; used in age-related information. This is given in the form 'YYYYMMDD'. each protocol will have a default coil; ge_functions works with the head coil, while ge_functionals128 works with the 8-channer coil echo shift of a protocol echo time, or TE, of the protocol Date and time when a session ended (can be approximate). Link between one session and another; used when we take an I/O slot to make-up for a lost fmri:NormalSession field of view in millimeters; given as a single value defining a square Field strength of a particular model of a scanner. Cannonically given in Tesla. flip angle of a protocol Gradient strength of a particular model of a scanner. String that describes whether or not the hospital was contacted regarding the aborting of a scan. @@TODO@@ We should rephrase this in order to better describe its meaning, which is to let, e.g., MGH know when a scan was aborted so that we keep track of lost time. A unique string that identifies the subject and is used to refer to the subject within the ontology. inversion time, or TI, of the protocol how much of k-space is covered; commonly "full" but can also be "7/8", "5/8", etc. Relates a scanner to a MRI coil. Relates an MRI scanner to a Manufacturer Relates a MRI Scanner to a particular scanner model. The full name of the subject; should not be used due to privacy concerns; see 'hasNameHash' instead. The full name of the subject, saved as a one-way hash. This is a privacy protection. The subject's name is encrypted by: 1) combining the name and a site-specific password by XOR; 2) taking this string and running it through the SHA1 mechanism. Thus the string is encrypted in a way such that an interested party much know the subject's name as well as the site-specific password in order to decode the information. Why is it necessary to this? We need to have some place where subjects' names are stored in order to tie the data to a particular person. As well, we'd like to be able to simply enter in a subject's name on a daily basis for day-to-day subject tracking. By encoding the name with a one-way mechanism we accomplish this goal while also protecting subject privacy. the total number of acquisitions for the protocol number of dummy scans used to let the scanner stabilize number of slices of a protocol connects an IRB to a particular protocol number ramp sampling of the protocol; not sure on the units raw image orientation of the protocol bandwidth, but commonly given in KHz/pixel repitition time, or TR, of the protocol Links a particular experiment with a researcher. Defines the type of MRI scanning run. String that describes any notes about a particular scan session; this is also where the experimenter can leave notes as to why a particular scan session was aborted. Links an experimental session to the type of session it was; the default is to assign all experimental sessions as fmri:NormalSession(s). Chromosomal sex of the person. Slew rate of a particular model of a scanner. slice acquisition order slice skip of the protocol; on Siemens scanners, this is given in percentage of the slice thickness, but here it is the actual numer of millimeters. slice thickness of the protocol Date and time when a session began (can be approximate). connects IRBs to particular study types, which will encompass a number (hopefully) of different studies. human readable name of the study; commonly will be an expanded form of the machine-readable rdf:ID for the study. connect studies to a larger taxonomy of study types. Links subjects to a particular experimental session. The weight of the subject; used for subject registration at the scanner. 1980-01-03 Nick Knouf 145.0 Links the coil used to the experimental session. Links a particular scanner (and the physical properties associated with it) to an experimental session. Links an individual run to a protocol definition. Boolean that determines whether or not a scanning session was completed.