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fix(appendix): Revise template-generated coordinate systems
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I've made several changes to the table of template identifiers:

  - [x] Reordered template identifiers alphabetically
  - [x] Removed the distinction between surface templates and volumetric
        templates. After all, to properly apply a surface template one
        should first spatially normalize to a particular volumetric
        template. Although it is possible to create mixed templates
        (e.g. using ``MNI152Lin`` to generate a mapping for volumetric
        coordinates and then, say, ``fsLR`` for the surface after some
        surface mapping process), this option should be discouraged.
        Anyways, this discussion does not affect how the names of BIDS
        entities should be specified, since one can always describe how
        the template coordinates are generated with the information
        described in this PR.
  - [x] Removed ``MNI152NLin6AsymConte69`` because it does not define
        any new coordinate system (see
        bids-standard#207 (comment)),
  - [x] Marked DEPRECATED ``fsaverage[3|4|5|6|sym]`
  - [x] Added ``fsaverage`` and ``fsaverageSym`` corresponding to such
        deprecations.
  - [x] Removed ``FS305`` as it is now covered by ``fsaverage``.
  - [x] DEPRECATED modifiers of ``UNCInfant``
  - [x] Reorganized subsections in "standard" vs "nonstandard" spaces.
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@oesteban
oesteban committed Aug 14, 2019
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60 changes: 23 additions & 37 deletions src/99-appendices/08-coordinate-systems.md
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Original file line number Diff line number Diff line change
Expand Up @@ -116,47 +116,33 @@ below, the origin is at the AC and the orientation of the axes is RAS. Unless
specified explicitly in the sidecar file in the `XXCoordinateSystemUnits` field,
the units are assumed to be mm.

### Common for Surface and Volume
### Standard template identifiers

| Coordinate System | Description |
| --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| ICBM452AirSpace | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml](http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml) |
| ICBM452Warp5Space | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml](http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml) |
| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) |
| fsaverage\[3|4|5|6|sym\] | (DEPRECATED, please use `fsaverage` plus internal modifiers to describe the density of the surface sampling. Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template |
| fsaverage | The `fsaverage` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of `MNI305` space. The `fsaverage` atlas also defines a surface reference system (formerly described as `fsaverage[3|4|5|6|sym]`). |
| fsLR | The `fsLR` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template correspond to `MNI152NLin6Asym`. Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image |
| MNIColin27 | Average of 27 T1 scans of a single subject [http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) |
| MNI152Lin | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) |
| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) |
| MNI152NLin2009\[a-c\]\[Sym|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) |
| MNI152NLin6ASym | A variation of `MNI152NLin6Sym` built by A. Janke that is released as the *MNI template* of FSL. Volumetric templates included with [HCP-Pipelines](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) correspond to this template too. [10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024) |
| MNI305 | Also known as avg305. |
| NIHPD | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) |
| OASIS30AntsOASISAnts | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) |
| OASIS30Atropos | [http://www.mindboggle.info/data.html](http://www.mindboggle.info/data.html) |
| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/) |
| UNCInfant | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) |

### Nonstandard template identifiers

| Coordinate System | Description |
| ----------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| individual | Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been refered to as `fsnative`. |
| custom | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. |

### Volume

| Coordinate System | Description |
| --------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| FS305 | FreeSurfer variant of the MNI305 space |
| MNI152Lin | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) |
| MNI152NLin6\[Sym|Asym\] | Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8 and FSL (MNI152NLin6Sym). [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) |
| MNI152NLin6AsymConte69 | Template based on MNI152NLin6Asym using Conte69 data. Built by Human Connectome Project. [https://github.com/Washington-University/HCPpipelines/tree/master/global/templates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) |
| MNI152NLin2009\[a-c\]\[Sym|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) |
| MNIColin27 | Average of 27 T1 scans of a single subject [http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) |
| MNI305 | Also known as avg305. |
| NIHPD | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) |
| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/) |
| OASIS30AntsOASISAnts | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) |
| OASIS30Atropos | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) |
| ICBM452AirSpace | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf) |
| ICBM452Warp5Space | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf) |
| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) |
| UNCInfant\[0|1|2\]V\[21|22|23\] | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) |

### Surface

| Coordinate System | Description |
| -------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| fsaverage\[3|4|5|6|sym\] | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template |
| fsLR\[164k|59k|32k|4k\] | Images were sampled to the 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image |

### Hybrid (Volume/Surface) aliases

Hybrid spaces combining surface and volume data used with CIFTI files.

| Coordinate System | Description |
| ----------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| HCPMNIfsLR32k | Combination of `MNI152NLin6AsymConte69` subcortical volumetric space (with 2mm grid) and `fsLR32k` surface space resulting in 91282 data points per timepoint. Used in Human Connectom Project. [https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates) |
| HCPMNIfsLR59k | Combination of `MNI152NLin6AsymConte69` subcortical volumetric space (with 1.6mm grid) and `fsLR59k` surface space resulting in 170494 data points per timepoint. Used in Human Connectom Project. [https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/170494_Greyordinates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/170494_Greyordinates) |

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