[ADD] Appendix - File collections

- For parametrically linked file collections
bids-standard · Nov 27, 2020 · 44e760f · 44e760f
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+# Appendix X: File collections
+
+To give context to the use of [parametrically linked file collections](./02-common-principles.md#file-name-structure), applications appealing to this common
+principle are listed by descriptive tables under their respective modalities.
+
+## Magnetic Resonance Imaging 
+
+### Anatomy imaging data 
+
+| Suffix  | Meta-data relevant entity | 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](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.20314)). Please visit the [qMRI appendix](#prioritylevels) for details                             |
+| IRT1    | inv                       | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22497)).                                                                                                                                                                                                                                                               |
+| MP2RAGE | flip, inv                 | 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](https://www.sciencedirect.com/science/article/pii/S1053811909010738?casa_token=u_CYBx4hi7IAAAAA:3w0cMTyU5jA1BdFs0s5oVcQeqF2tZho0iJ9d4N1kExfaX27v9-JnWacF6mbEp_lMKZ64CvoTl8k)                                                               |
+| 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](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.21732)).                                                                                                               |
+| MPM     | flip, mt                  | 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](https://www.frontiersin.org/articles/10.3389/fnins.2013.00095/full)). See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols. |