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---
# This file defines valid BIDS file suffixes.
# For rules regarding how suffixes relate to datatypes, see files in `rules/files/raw/`.
TwoPE:
value: 2PE
display_name: 2-photon excitation microscopy
description: |
2-photon excitation microscopy imaging data
BF:
value: BF
display_name: Bright-field microscopy
description: |
Bright-field microscopy imaging data
Chimap:
value: Chimap
display_name: Quantitative susceptibility map (QSM)
description: |
In parts per million (ppm).
QSM allows for determining the underlying magnetic susceptibility of tissue
(Chi)
([Wang & Liu, 2014](https://doi.org/10.1002/mrm.25358)).
Chi maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: ppm
CARS:
value: CARS
display_name: Coherent anti-Stokes Raman spectroscopy
description: |
Coherent anti-Stokes Raman spectroscopy imaging data
CONF:
value: CONF
display_name: Confocal microscopy
description: |
Confocal microscopy imaging data
DIC:
value: DIC
display_name: Differential interference contrast microscopy
description: |
Differential interference contrast microscopy imaging data
DF:
value: DF
display_name: Dark-field microscopy
description: |
Dark-field microscopy imaging data
FLAIR:
value: FLAIR
display_name: Fluid attenuated inversion recovery image
description: |
In arbitrary units (arbitrary).
Structural images with predominant T2 contribution (also known as T2-FLAIR),
in which signal from fluids (for example, CSF) is nulled out by adjusting
inversion time, coupled with notably long repetition and echo times.
unit: arbitrary
FLASH:
value: FLASH
display_name: Fast-Low-Angle-Shot image
description: |
FLASH (Fast-Low-Angle-Shot) is a vendor-specific implementation for spoiled
gradient echo acquisition.
It is commonly used for rapid anatomical imaging and also for many different
qMRI applications.
When used for a single file, it does not convey any information about the
image contrast.
When used in a file collection, it may result in conflicts across filenames of
different applications.
**Change:** Removed from suffixes.
FLUO:
value: FLUO
display_name: Fluorescence microscopy
description: |
Fluorescence microscopy imaging data
IRT1:
value: IRT1
display_name: Inversion recovery T1 mapping
description: |
The IRT1 method involves multiple inversion recovery spin-echo images
acquired at different inversion times
([Barral et al. 2010](https://doi.org/10.1002/mrm.22497)).
M0map:
value: M0map
display_name: Equilibrium magnetization (M0) map
description: |
In arbitrary units (arbitrary).
A common quantitative MRI (qMRI) fitting variable that represents the amount
of magnetization at thermal equilibrium.
M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications
(for example, variable flip angle T1 mapping).
unit: arbitrary
MEGRE:
value: MEGRE
display_name: Multi-echo Gradient Recalled Echo
description: |
Anatomical gradient echo images acquired at different echo times.
Please note that this suffix is not intended for the logical grouping of
images acquired using an Echo Planar Imaging (EPI) readout.
MESE:
value: MESE
display_name: Multi-echo Spin Echo
description: |
The MESE method involves multiple spin echo images acquired at different echo
times and is primarily used for T2 mapping.
Please note that this suffix is not intended for the logical grouping of
images acquired using an Echo Planar Imaging (EPI) readout.
MP2RAGE:
value: MP2RAGE
display_name: Magnetization Prepared Two Gradient Echoes
description: |
The MP2RAGE method is a special protocol that collects several images at
different flip angles and inversion times to create a parametric T1map by
combining the magnitude and phase images
([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).
MPE:
value: MPE
display_name: Multi-photon excitation microscopy
description: |
Multi-photon excitation microscopy imaging data
MPM:
value: MPM
display_name: Multi-parametric Mapping
description: |
The MPM approaches (a.k.a hMRI) involves the acquisition of highly-similar
anatomical images that differ in terms of application of a magnetization
transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and
magnitue/phase parts
([Weiskopf et al. 2013](https://doi.org/10.3389/fnins.2013.00095)).
See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for
suggested MPM acquisition protocols.
MTR:
value: MTR
display_name: Magnetization Transfer Ratio
description: |
This method is to calculate a semi-quantitative magnetization transfer ratio
map.
MTRmap:
value: MTRmap
display_name: Magnetization transfer ratio image
description: |
In arbitrary units (arbitrary).
MTR maps are REQUIRED to use this suffix regardless of the method used to
generate them.
MTRmap intensity values are RECOMMENDED to be represented in percentage in
the range of 0-100%.
unit: arbitrary
minValue: 0
maxValue: 100
MTS:
value: MTS
display_name: Magnetization transfer saturation
description: |
This method is to calculate a semi-quantitative magnetization transfer
saturation index map.
The MTS method involves three sets of anatomical images that differ in terms
of application of a magnetization transfer RF pulse (MTon or MToff) and flip
angle ([Helms et al. 2008](https://doi.org/10.1002/mrm.21732)).
MTVmap:
value: MTVmap
display_name: Macromolecular tissue volume (MTV) image
description: |
In arbitrary units (arbitrary).
MTV maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: arbitrary
MTsat:
value: MTsat
display_name: Magnetization transfer saturation image
description: |
In arbitrary units (arbitrary).
MTsat maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: arbitrary
MWFmap:
value: MWFmap
display_name: Myelin water fraction image
description: |
In arbitrary units (arbitrary).
MWF maps are REQUIRED to use this suffix regardless of the method used to
generate them.
MWF intensity values are RECOMMENDED to be represented in percentage in the
range of 0-100%.
unit: arbitrary
minValue: 0
maxValue: 100
NLO:
value: NLO
display_name: Nonlinear optical microscopy
description: |
Nonlinear optical microscopy imaging data
OCT:
value: OCT
display_name: Optical coherence tomography
description: |
Optical coherence tomography imaging data
PC:
value: PC
display_name: Phase-contrast microscopy
description: |
Phase-contrast microscopy imaging data
PD:
value: PD
display_name: Proton density image
description: |
Ambiguous, may refer to a parametric image or to a conventional image.
**Change:** Replaced by `PDw` or `PDmap`.
unit: arbitrary
PDT2:
value: PDT2
display_name: PD and T2 weighted image
description: |
In arbitrary units (arbitrary).
A two-volume 4D image, where the volumes are, respectively, PDw and T2w
images acquired simultaneously.
If separated into 3D volumes, the `PDw` and `T2w` suffixes SHOULD be used instead,
and an acquisition entity MAY be used to distinguish the images from others with
the same suffix, for example, `acq-PDT2_PDw.nii` and `acq-PDT2_T2w.nii`.
unit: arbitrary
PDmap:
value: PDmap
display_name: Proton density image
description: |
In arbitrary units (arbitrary).
PD maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: arbitrary
PDw:
value: PDw
display_name: Proton density (PD) weighted image
description: |
In arbitrary units (arbitrary).
The contrast of these images is mainly determined by spatial variations in
the spin density (1H) of the imaged specimen.
This contrast is achieved at short echo times and long repetition times;
for gradient echo, this weighting is also possible with a short TR (TR<<T1) and a small flip angle.
unit: arbitrary
PLI:
value: PLI
display_name: Polarized-light microscopy
description: |
Polarized-light microscopy imaging data
R1map:
value: R1map
display_name: Longitudinal relaxation rate image
description: |
In seconds<sup>-1</sup> (1/s).
R1 maps (R1 = 1/T1) are REQUIRED to use this suffix regardless of the method
used to generate them.
unit: 1/s
R2map:
value: R2map
display_name: True transverse relaxation rate image
description: |
In seconds<sup>-1</sup> (1/s).
R2 maps (R2 = 1/T2) are REQUIRED to use this suffix regardless of the method
used to generate them.
unit: 1/s
R2starmap:
value: R2starmap
display_name: Observed transverse relaxation rate image
description: |
In seconds<sup>-1</sup> (1/s).
R2-star maps (R2star = 1/T2star) are REQUIRED to use this suffix regardless
of the method used to generate them.
unit: 1/s
RB1COR:
value: RB1COR
display_name: RB1COR
description: |
Low resolution images acquired by the body coil
(in the gantry of the scanner) and the head coil using identical acquisition
parameters to generate a combined sensitivity map as described in
[Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).
RB1map:
value: RB1map
display_name: RF receive sensitivity map
description: |
In arbitrary units (arbitrary).
Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this
suffix regardless of the method used to generate them.
RB1map intensity values are RECOMMENDED to be represented as percent
multiplicative factors such that Amplitude<sub>effective</sub> =
B1-<sub>intensity</sub>\*Amplitude<sub>ideal</sub>.
unit: arbitrary
S0map:
value: S0map
display_name: Observed signal amplitude (S0) image
description: |
In arbitrary units (arbitrary).
For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal
before exponential (T2-star) signal decay.
In other words: the exponential of the intercept for a linear decay model
across log-transformed echos. For more information, please see, for example,
[the tedana documentation](https://tedana.readthedocs.io/en/latest/\
approach.html#monoexponential-decay-model-fit).
S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset.
SEM:
value: SEM
display_name: Scanning electron microscopy
description: |
Scanning electron microscopy imaging data
SPIM:
value: SPIM
display_name: Selective plane illumination microscopy
description: |
Selective plane illumination microscopy imaging data
SR:
value: SR
display_name: Super-resolution microscopy
description: |
Super-resolution microscopy imaging data
T1map:
value: T1map
display_name: Longitudinal relaxation time image
description: |
In seconds (s).
T1 maps are REQUIRED to use this suffix regardless of the method used to
generate them.
See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro)
for further reading on T1-mapping.
unit: s
T1rho:
value: T1rho
display_name: T1 in rotating frame (T1 rho) image
description: |
In seconds (s).
T1-rho maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: s
T1w:
value: T1w
display_name: T1-weighted image
description: |
In arbitrary units (arbitrary).
The contrast of these images is mainly determined by spatial variations in
the longitudinal relaxation time of the imaged specimen.
In spin-echo sequences this contrast is achieved at relatively short
repetition and echo times.
To achieve this weighting in gradient-echo images, again, short repetition
and echo times are selected; however, at relatively large flip angles.
Another common approach to increase T1 weighting in gradient-echo images is
to add an inversion preparation block to the beginning of the imaging
sequence (for example, `TurboFLASH` or `MP-RAGE`).
unit: arbitrary
T2map:
value: T2map
display_name: True transverse relaxation time image
description: |
In seconds (s).
T2 maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: s
T2star:
value: T2star
display_name: T2\* image
description: |
Ambiguous, may refer to a parametric image or to a conventional image.
**Change:** Replaced by `T2starw` or `T2starmap`.
anyOf:
- unit: arbitrary
- unit: s
T2starmap:
value: T2starmap
display_name: Observed transverse relaxation time image
description: |
In seconds (s).
T2-star maps are REQUIRED to use this suffix regardless of the method used to
generate them.
unit: s
T2starw:
value: T2starw
display_name: T2star weighted image
description: |
In arbitrary units (arbitrary).
The contrast of these images is mainly determined by spatial variations in
the (observed) transverse relaxation time of the imaged specimen.
In spin-echo sequences, this effect is negated as the excitation is followed
by an inversion pulse.
The contrast of gradient-echo images natively depends on T2-star effects.
However, for T2-star variation to dominate the image contrast,
gradient-echo acquisitions are carried out at long repetition and echo times,
and at small flip angles.
unit: arbitrary
T2w:
value: T2w
display_name: T2-weighted image
description: |
In arbitrary units (arbitrary).
The contrast of these images is mainly determined by spatial variations in
the (true) transverse relaxation time of the imaged specimen.
In spin-echo sequences this contrast is achieved at relatively long
repetition and echo times.
Generally, gradient echo sequences are not the most suitable option for
achieving T2 weighting, as their contrast natively depends on T2-star rather
than on T2.
unit: arbitrary
TB1AFI:
value: TB1AFI
display_name: TB1AFI
description: |
This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120))
calculates a B1<sup>+</sup> map from two images acquired at interleaved (two)
TRs with identical RF pulses using a steady-state sequence.
TB1DAM:
value: TB1DAM
display_name: TB1DAM
description: |
The double-angle B1<sup>+</sup> method
([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based
on the calculation of the actual angles from signal ratios,
collected by two acquisitions at different nominal excitation flip angles.
Common sequence types for this application include spin echo and echo planar
imaging.
TB1EPI:
value: TB1EPI
display_name: TB1EPI
description: |
This B1<sup>+</sup> mapping method
([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two
EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at
multiple flip angles in one sequence, used in the calculation of deviations
from the nominal flip angle.
TB1RFM:
value: TB1RFM
display_name: TB1RFM
description: |
The result of a Siemens `rf_map` product sequence.
This sequence produces two images.
The first image appears like an anatomical image and the second output is a
scaled flip angle map.
TB1SRGE:
value: TB1SRGE
display_name: TB1SRGE
description: |
Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of
two saturation recovery images with different time delays,
and a simulated look-up table to estimate B1+
([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)).
This sequence can also be used in conjunction with MP2RAGE T1 mapping to
iteratively improve B1+ and T1 map estimation
([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)).
TB1TFL:
value: TB1TFL
display_name: TB1TFL
description: |
The result of a Siemens `tfl_b1_map` product sequence.
This sequence produces two images.
The first image appears like an anatomical image and the second output is a
scaled flip angle map.
TB1map:
value: TB1map
display_name: RF transmit field image
description: |
In arbitrary units (arbitrary).
Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this
suffix regardless of the method used to generate them.
TB1map intensity values are RECOMMENDED to be represented as percent
multiplicative factors such that FlipAngle<sub>effective</sub> =
B1+<sub>intensity</sub>\*FlipAngle<sub>nominal</sub> .
unit: arbitrary
TEM:
value: TEM
display_name: Transmission electron microscopy
description: |
Transmission electron microscopy imaging data
UNIT1:
value: UNIT1
display_name: Homogeneous (flat) T1-weighted MP2RAGE image
description: |
In arbitrary units (arbitrary).
UNIT1 images are REQUIRED to use this suffix regardless of the method used to
generate them.
Note that although this image is T1-weighted, regions without MR signal will
contain white salt-and-pepper noise that most segmentation algorithms will
fail on.
Therefore, it is important to dissociate it from `T1w`.
Please see [`MP2RAGE` specific notes](SPEC_ROOT/appendices/qmri.md#unit1-images)
in the qMRI appendix for further information.
VFA:
value: VFA
display_name: Variable flip angle
description: |
The VFA method involves at least two spoiled gradient echo (SPGR) of
steady-state free precession (SSFP) images acquired at different flip angles.
Depending on the provided metadata fields and the sequence type,
data may be eligible for DESPOT1, DESPOT2 and their variants
([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).
angio:
value: angio
display_name: Angiogram
description: |
Magnetic resonance angiography sequences focus on enhancing the contrast of
blood vessels (generally arteries, but sometimes veins) against other tissue
types.
asl:
value: asl
display_name: Arterial Spin Labeling
description: |
The complete ASL time series stored as a 4D NIfTI file in the original
acquisition order, with possible volume types including: control, label,
m0scan, deltam, cbf.
aslcontext:
value: aslcontext
display_name: Arterial Spin Labeling Context
description: |
A TSV file defining the image types for volumes in an associated ASL file.
asllabeling:
value: asllabeling
display_name: ASL Labeling Screenshot
description: |
An anonymized screenshot of the planning of the labeling slab/plane
with respect to the imaging slab or slices.
This screenshot is based on DICOM macro C.8.13.5.14.
beh:
value: beh
display_name: Behavioral recording
description: |
Behavioral recordings from tasks.
These files are similar to events files, but do not include the `"onset"` and
`"duration"` columns that are mandatory for events files.
blood:
value: blood
display_name: Blood recording data
description: |
Blood measurements of radioactivity stored in
[tabular files](SPEC_ROOT/common-principles.md#tabular-files)
and located in the `pet/` directory along with the corresponding PET data.
bold:
value: bold
display_name: Blood-Oxygen-Level Dependent image
description: |
Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)
cbv:
value: cbv
display_name: Cerebral blood volume image
description: |
Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)
channels:
value: channels
display_name: Channels File
description: |
Channel information.
coordsystem:
value: coordsystem
display_name: Coordinate System File
description: |
A JSON document specifying the coordinate system(s) used for the MEG, EEG,
head localization coils, and anatomical landmarks.
defacemask:
value: defacemask
display_name: Defacing Mask
description: |
A binary mask that was used to remove facial features from an anatomical MRI
image.
dseg:
value: dseg
display_name: Discrete Segmentation
description: |
A discrete segmentation.
This suffix may only be used in derivative datasets.
dwi:
value: dwi
display_name: Diffusion-weighted image
description: |
Diffusion-weighted imaging contrast (specialized T2 weighting).
eeg:
value: eeg
display_name: Electroencephalography
description: |
Electroencephalography recording data.
electrodes:
value: electrodes
display_name: Electrodes
description: |
File that gives the location of (i)EEG electrodes.
ephys:
value: ephys
display_name: Electrophysiology
description: |
Extra- or intracellular microelectrode recording data.
epi:
value: epi
display_name: EPI
description: |
The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo
EPI scans with different phase encoding directions to estimate the underlying
inhomogeneity/deformation map.
events:
value: events
display_name: Events
description: |
Event timing information from a behavioral task.
fieldmap:
value: fieldmap
display_name: Fieldmap
description: |
Some MR schemes such as spiral-echo imaging (SEI) sequences are able to
directly provide maps of the *B<sub>0</sub>* field inhomogeneity.
headshape:
value: headshape
display_name: Headshape File
description: |
The 3-D locations of points that describe the head shape and/or electrode
locations can be digitized and stored in separate files.
ieeg:
value: ieeg
display_name: Intracranial Electroencephalography
description: |
Intracranial electroencephalography recording data.
inplaneT1:
value: inplaneT1
display_name: Inplane T1
description: |
In arbitrary units (arbitrary).
T1 weighted structural image matched to a functional (task) image.
unit: arbitrary
inplaneT2:
value: inplaneT2
display_name: Inplane T2
description: |
In arbitrary units (arbitrary).
T2 weighted structural image matched to a functional (task) image.
unit: arbitrary
m0scan:
value: m0scan
display_name: M0 image
description: |
The M0 image is a calibration image, used to estimate the equilibrium
magnetization of blood.
magnitude:
value: magnitude
display_name: Magnitude
description: |
Field-mapping MR schemes such as gradient-recalled echo (GRE) generate a
Magnitude image to be used for anatomical reference.
Requires the existence of Phase, Phase-difference or Fieldmap maps.
magnitude1:
value: magnitude1
display_name: Magnitude
description: |
Magnitude map generated by GRE or similar schemes, associated with the first
echo in the sequence.
magnitude2:
value: magnitude2
display_name: Magnitude
description: |
Magnitude map generated by GRE or similar schemes, associated with the second
echo in the sequence.
markers:
value: markers
display_name: MEG Sensor Coil Positions
description: |
Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh
system, which saves the MEG sensor coil positions in a separate file with two
possible filename extensions (`.sqd`, `.mrk`).
For these files, the `markers` suffix MUST be used.
For example: `sub-01_task-nback_markers.sqd`
mask:
value: mask
display_name: Binary Mask
description: |
A binary mask that functions as a discrete "label" for a single structure.
This suffix may only be used in derivative datasets.
meg:
value: meg
display_name: Magnetoencephalography
description: |
Unprocessed MEG data stored in the native file format of the MEG instrument
with which the data was collected.
motion:
value: motion
display_name: Motion
description: |
Data recorded from a tracking system store.
nirs:
value: nirs
display_name: Near Infrared Spectroscopy
description: Data associated with a Shared Near Infrared Spectroscopy Format file.
optodes:
value: optodes
display_name: Optodes
description: |
Either a light emitting device, sometimes called a transmitter, or a photoelectric transducer, sometimes called a
receiver.
pet:
value: pet
display_name: Positron Emission Tomography
description: |
PET imaging data SHOULD be stored in 4D
(or 3D, if only one volume was acquired) NIfTI files with the `_pet` suffix.
Volumes MUST be stored in chronological order
(the order they were acquired in).
phase:
value: phase
display_name: Phase image
description: |
[DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
Phase information associated with magnitude information stored in BOLD
contrast.
This suffix should be replaced by the
[`part-phase`](SPEC_ROOT/appendices/entities.md#part)
in conjunction with the `bold` suffix.
anyOf:
- unit: arbitrary
- unit: rad
phase1:
value: phase1
display_name: Phase
description: |
Phase map generated by GRE or similar schemes, associated with the first
echo in the sequence.
phase2:
value: phase2
display_name: Phase
description: |
Phase map generated by GRE or similar schemes, associated with the second
echo in the sequence.
phasediff:
value: phasediff
display_name: Phase-difference
description: |
Some scanners subtract the `phase1` from the `phase2` map and generate a
unique `phasediff` file.
For instance, this is a common output for the built-in fieldmap sequence of
Siemens scanners.
photo:
value: photo
display_name: Photo File
description: |
Photos of the anatomical landmarks, head localization coils or tissue sample.
physio:
value: physio
display_name: Physiological recording
description: |
Physiological recordings such as cardiac and respiratory signals.
probe:
value: probe
display_name: A recording probe
description: |
A probe with one or more recording contacts.
probseg:
value: probseg
display_name: Probabilistic Segmentation
description: |
A probabilistic segmentation.
This suffix may only be used in derivative datasets.
sbref:
value: sbref
display_name: Single-band reference image
description: |
Single-band reference for one or more multi-band `dwi` images.
scans:
value: scans
display_name: Scans file
description: |
The purpose of this file is to describe timing and other properties of each imaging acquisition
sequence (each run file) within one session.
Each neural recording file SHOULD be described by exactly one row. Some recordings consist of
multiple parts, that span several files, for example through echo-, part-, or split- entities.
Such recordings MUST be documented with one row per file.
Relative paths to files should be used under a compulsory filename header.
If acquisition time is included it should be listed under the acq_time header.
Acquisition time refers to when the first data point in each run was acquired.
Furthermore, if this header is provided, the acquisition times of all files that belong to a
recording MUST be identical.
Datetime should be expressed as described in Units.
Additional fields can include external behavioral measures relevant to the scan.
For example vigilance questionnaire score administered after a resting state scan.
All such included additional fields SHOULD be documented in an accompanying _scans.json file
that describes these fields in detail (see Tabular files).
sessions:
value: sessions
display_name: Sessions file
description: |
In case of multiple sessions there is an option of adding additional sessions.tsv files
describing variables changing between sessions.
In such case one file per participant SHOULD be added.
These files MUST include a session_id column and describe each session by one and only one row.
Column names in sessions.tsv files MUST be different from group level participant key column
names in the participants.tsv file.
stim:
value: stim
display_name: Continuous recording
description: |
Continuous measures, such as parameters of a film or audio stimulus.
uCT:
value: uCT
display_name: Micro-CT
description: |
Micro-CT imaging data