Appendix X: File collections

Here, some concrete use-cases of entity-linked file collections are listed using descriptive tables, organized by modality.

The tables in this appendix catalog applications where the use of a file collection is REQUIRED.

Certain entitites interlink the files in a file collection through a metadata field. Unlike other common entities (for example run), they require an iteration over different values of the metadata fields they represent. Please keep the following list of linking entities up-to-date with the file collections included in this appendix:

• Magnetic Resonance Imaging
  • echo
  • flip
  • inv
  • mt
  • part

Magnetic Resonance Imaging

Anatomy imaging data

Template:

sub-<label>/[ses-<label>/]
    anat/
        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]

Suffix	Linking entities	Application	Description
VFA	flip	Variable flip angle	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).
IRT1	inv, part	Inversion recovery T1 mapping	The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times (Barral et al. 2010).
MP2RAGE	flip, inv, echo, part	Magnetization prepared two gradient echoes	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).
MESE	echo	Multi-echo spin-echo	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.
MEGRE	echo	Multi-echo gradient-echo	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.
MTR	mt	Magnetization transfer ratio	This method is to calculate a semi-quantitative magnetization transfer ratio map.
MTS	flip, mt	Magnetization transfer saturation	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).
MPM	flip, mt, echo, part	Multi-parametric mapping	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). See here for suggested MPM acquisition protocols.

Fieldmap data

sub-<label>/[ses-<label>/]
    fmap/
        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]

Suffix	Meta-data relevant entity	Application	Description
TB1DAM	flip	Double-angle B1+ mapping	The double-angle B1+ method (Insko and Bolinger 1993) 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	flip, echo	B1+ mapping with 3D EPI	This B1+ mapping method (Jiru and Klose 2006) 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.
TB1AFI	Please see the qMRI appendix.	Actual Flip Angle Imaging (AFI)	This method (Yarnykh 2007) calculates a B1+ map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.
TB1TFL	Please see the qMRI appendix.	Siemens tfl_b1_map	B1+ data acquired using tfl_b1_map product sequence by Siemens based on the method by Chung et al. (2010). The sequence generates one anatomical image and one scaled flip angle map.
TB1RFM	Please see the qMRI appendix.	Siemens rf_map	B1+ data acquired using rf_map product sequence by Siemens.
TB1SRGE	flip, inv	SA2RAGE	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). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation (Marques & Gruetter 2013).
RB1COR	Please see the qMRI appendix.	B1- field correction	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).