Clinical Imaging Modalities

MRI

Related files:

📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

This schema is for clinical imaging using magnetic resonance imaging (MRI).

Metadata schema

Version 1 (use this one)

Shared by all types

version
description
donor_id
tissue_id
execution_datetime
protocols_io_doi
operator
operator_email
pi
pi_email
assay_category
assay_type
acquisition_instrument_vendor
acquisition_instrument_model

Shared by all clinical imaging assays

single_file_export_format
max_x_width_value
max_x_width_unit
max_y_height_value
max_y_height_unit
roi_description
roi_id
resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
resolution_z_value
resolution_z_unit
pixel_size_z_value
pixel_size_z_unit
number_of_images

Unique to this type

frequency_value
frequency_unit
coil
field_strength_value
field_strength_unit
scanning_sequence
sequence_variant
echo_time
repetition_time
flip_angle
echo_train_length
acquisition_matrix_size_in_frequency_encoding_direction
acquisition_matrix_size_in_phase_encoding_direction
number_of_image_rows
number_of_image_columns
number_of_averages
contributors_path
data_path

Shared by all types

`version`

Version of the schema to use when validating this metadata.

constraint	value
enum	`1`
required	`True`

`description`

Free-text description of this assay.

constraint	value
required	`True`

`donor_id`

HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.

constraint	value
pattern (regular expression)	`[A-Z]+[0-9]+`
required	`True`

`tissue_id`

HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.

constraint	value
pattern (regular expression)	`(([A-Z]+[0-9]+)-[A-Z]{2}\d(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d(-\d+)+(_\d+)?)*`
required	`True`

Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.

constraint	value
type	`datetime`
format	`%Y-%m-%d %H:%M`
required	`True`

`protocols_io_doi`

DOI for protocols.io referring to the protocol for this assay.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`operator`

Name of the person responsible for executing the assay.

constraint	value
required	`True`

`operator_email`

Email address for the operator.

constraint	value
format	`email`
required	`True`

`pi`

Name of the principal investigator responsible for the data.

constraint	value
required	`True`

`pi_email`

Email address for the principal investigator.

constraint	value
format	`email`
required	`True`

`assay_category`

Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.

constraint	value
enum	`clinical_imaging`
required	`True`

`assay_type`

The specific type of assay being executed.

constraint	value
enum	`MRI`
required	`True`

`acquisition_instrument_vendor`

An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.

constraint	value
required	`True`

`acquisition_instrument_model`

Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.

constraint	value
required	`True`

Shared by all clinical imaging assays

`single_file_export_format`

The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.)

constraint	value
required	`True`

`max_x_width_value`

Image width value of the ROI acquisition.

constraint	value
type	`number`
required	`True`

`max_x_width_unit`

Units of image width of the ROI acquisition. Leave blank if not applicable.

constraint	value
enum	`um` or `mm`
required	`False`
required if	`max_x_width_value` present

`max_y_height_value`

Image height value of the ROI acquisition.

constraint	value
type	`number`
required	`True`

`max_y_height_unit`

Units of image height of the ROI acquisition. Leave blank if not applicable.

constraint	value
enum	`um` or `mm`
required	`False`
required if	`max_y_height_value` present

`roi_description`

A description of the region of interest (ROI) captured in the image.

constraint	value
required	`True`

`roi_id`

Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`
minimum	`1`

`resolution_x_value`

The width of a pixel.

constraint	value
type	`number`
required	`True`

`resolution_x_unit`

The unit of measurement of the width of a pixel. Leave blank if not applicable.

constraint	value
enum	`nm`, `um`, or `mm`
required	`False`
required if	`resolution_x_value` present

`resolution_y_value`

The height of a pixel.

constraint	value
type	`number`
required	`True`

`resolution_y_unit`

The unit of measurement of the height of a pixel. Leave blank if not applicable.

constraint	value
enum	`nm`, `um`, or `mm`
required	`False`
required if	`resolution_y_value` present

`resolution_z_value`

Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`resolution_z_unit`

The unit of incremental distance between image slices.(um) Leave blank if not applicable.

constraint	value
enum	`nm`, `um`, or `mm`
required	`False`
required if	`resolution_z_value` present

`pixel_size_z_value`

Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`pixel_size_z_unit`

Depth unit of the pixel or voxel measurement. Leave blank if not applicable.

constraint	value
enum	`nm`, `um`, or `mm`
required	`False`
required if	`pixel_size_z_value` present

`number_of_images`

The total number of images in the dataset.

constraint	value
type	`integer`
required	`True`

Unique to this type

`frequency_value`

Frequency at which the imaging device is operating. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`frequency_unit`

Unit of frequency at which the imaging device is operating. Example: Hz, kHz, MHz. Leave blank if not applicable.

constraint	value
required	`False`
enum	`Hz`, `kHz`, or `MHz`
required if	`frequency_value` present

`coil`

Receiver coil name used to collect MRI data. Example: 32 channel body coil. Leave blank if not applicable.

constraint	value
required	`False`

`field_strength_value`

MRI scanner magnetic field strength value. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`field_strength_unit`

MRI scanner magnetic field strength in units of Tesla [T]. Leave blank if not applicable.

constraint	value
required	`False`
enum	`Tesla`
required if	`field_strength_value` present

`scanning_sequence`

Pulse sequence used to collect MRI data. Leave blank if not applicable.

constraint	value
required	`False`
enum	`spin echo`, `inversion recovery`, `gradient echo`, `echo planar`, or `research mode`

`sequence_variant`

Variant of the Scanning Sequence. Leave blank if not applicable.

constraint	value
required	`False`
enum	`segmented k-space`, `magnetization transfer contrast`, `steady state`, `time reversed steady state`, `spoiled`, `magnetization prepared`, `oversampling phase`, or `no sequence variant`

`echo_time`

Time in msec between the middle of the excitation pulse and the peak of the echo produced (kx=0). In the case of segmented k-space, the TE(eff) is the time between the middle of the excitation pulse to the peak of the echo that is used to cover the center of k-space (i.e., -kx=0, ky=0). Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`repetition_time`

The period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence. Leave blank if not applicable.

constraint	value
type	`number`
required	`False`

`flip_angle`

Steady state angle in degrees to which the magnetic vector is flipped from the magnetic vector of the primary field. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`echo_train_length`

Number of lines in k-space acquired per excitation per image. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`acquisition_matrix_size_in_frequency_encoding_direction`

Dimensions of the acquired frequency data before reconstruction. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`acquisition_matrix_size_in_phase_encoding_direction`

Dimensions of the acquired phase data before reconstruction, per image. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`number_of_image_rows`

Number of rows of the reconstructed data, per image. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`number_of_image_columns`

Number of columns of the reconstructed data. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`number_of_averages`

Number of times a given pulse sequence is repeated in the collection of a single image or volume. Leave blank if not applicable.

constraint	value
type	`integer`
required	`False`

`contributors_path`

Relative path to file with ORCID IDs for contributors for this dataset.

constraint	value
required	`True`

`data_path`

Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.

constraint	value
required	`True`