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# Appendix X: File collections

To give context to the use of [entity-linked file collections](./02-common-principles.md#file-name-structure), applications concerned with this
To give context to the use of [entity-linked file collections](../02-common-principles.md#file-name-structure), applications concerned with this
common principle are listed by descriptive tables under their respective modalities.

Note that the tables in this appendix catalog applications where the use of
Note that 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 (e.g. `run`), they require an iteration over different
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`](./99-appendices/09-entities.md#echo)
* Magnetic Resonance Imaging
* [`echo`](./09-entities.md#echo)
* `flip` (to be added)
* `inv` (to be added)
* `mt` (to be added)
* `mt` (to be added)
* `part` (to be added)

## Magnetic Resonance Imaging
## Magnetic Resonance Imaging

### Anatomy imaging data
### Anatomy imaging data

| Suffix | Linking entities | Application | Description |
| 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](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.20314)). |
| 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](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22497)). |
| 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](https://www.sciencedirect.com/science/article/pii/S1053811909010738?casa_token=u_CYBx4hi7IAAAAA:3w0cMTyU5jA1BdFs0s5oVcQeqF2tZho0iJ9d4N1kExfaX27v9-JnWacF6mbEp_lMKZ64CvoTl8k) |
| 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)). |
| 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](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22497)). |
| 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](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, 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](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. |
| 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](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. |

### Fieldmap data

Expand All @@ -47,7 +47,7 @@ included in this appendix:

\* These file collections call for the use of special notations that cannot
be resolved by entities that can generalize to other applications. Instead of
introducing an entity that is exclusive to a single application, method developers
who commonly use these file collections for the `MPM` application reached the consensus
on the use of `acq` entity to distinguish individual files. Please visit the qMRI
introducing an entity that is exclusive to a single application, method developers
who commonly use these file collections for the `MPM` application reached the consensus
on the use of `acq` entity to distinguish individual files. Please visit the qMRI
appendix for further details.

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