diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index c3312a3e70..8cf00dc6b7 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -196,25 +196,25 @@ Unless specified explicitly in the sidecar file in the ### Standard template identifiers -| **Coordinate System** | **Description** | **Used by** | **Reference** | -| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | -| 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/research/atlases](https://www.loni.usc.edu/research/atlases) | -| 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/research/atlases](https://www.loni.usc.edu/research/atlases) | -| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452. | SPM12 | [https://brain-development.org/](https://brain-development.org/) | -| 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\[3\|4\|5\|6\|sym\]). | Freesurfer | | -| fsaverageSym | 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 `fsaverageSym` atlas also defines a symmetric surface reference system (formerly described as `fsaveragesym`). | Freesurfer | | -| fsLR | The `fsLR` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds 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. | Freesurfer | | -| MNIColin27 | Average of 27 T1 scans of a single subject | SPM96 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | -| MNI152Lin | Also known as ICBM (version with linear coregistration) | SPM99 to SPM8 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) | -| MNI152NLin2009\[a-c\]\[Sym\|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavors each in symmetric or asymmetric version. | DARTEL toolbox in SPM12b | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | -| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). | FSL | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) | -| 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) correspond to this template too. | HCP-Pipelines | [doi: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. | | [https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | -| OASIS30AntsOASISAnts | | | [https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436) | -| OASIS30Atropos | | | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) | -| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. | | [http://talairach.org/](http://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) | +| **Coordinate System** | **Description** | **Used by** | **Reference** | +| ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| 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/research/atlases](https://www.loni.usc.edu/research/atlases) | +| 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/research/atlases](https://www.loni.usc.edu/research/atlases) | +| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452. | SPM12 | [https://brain-development.org/](https://brain-development.org/) | +| fsaverage | The `fsaverage` is a surface reference system (formerly described as fsaverage\[3\|4\|5\|6\|sym\]). Additionally, by convention, `fsaverage` is used as shorthand for a **dual template** providing both volumetric and surface coordinates references, where the surface template is `fsaverage` and the volumetric template corresponds to a FreeSurfer variant of `MNI305` space. | Freesurfer | | +| fsaverageSym | The `fsaverageSym` is a symmetric surface reference system (formerly described as `fsaveragesym`). Additionally, by convention, `fsaverageSym` is used as shorthand for a **dual template** providing both volumetric and surface coordinates references, where the surface template is `fsaverageSym` and the volumetric template corresponds to a FreeSurfer variant of `MNI305` space. | Freesurfer | | +| fsLR | The `fsLR` is a surface template. Additionally, by convention, `fsLR` is used as shorthand for a **dual template** providing both volumetric and surface coordinates references, where the surface template is `fsLR` and the volumetric template corresponds 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. | Freesurfer | | +| MNIColin27 | Average of 27 T1 scans of a single subject | SPM96 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | +| MNI152Lin | Also known as ICBM (version with linear coregistration) | SPM99 to SPM8 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) | +| MNI152NLin2009\[a-c\]\[Sym\|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavors each in symmetric or asymmetric version. | DARTEL toolbox in SPM12b | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | +| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). | FSL | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) | +| 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) correspond to this template too. | HCP-Pipelines | [doi: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. | | [https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | +| OASIS30AntsOASISAnts | | | [https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436) | +| OASIS30Atropos | | | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) | +| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. | | [http://talairach.org/](http://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) | The following template identifiers are retained for backwards compatibility of BIDS implementations. diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index d2da4fd509..b49caf0073 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -405,34 +405,44 @@ fsaverage: value: fsaverage display_name: fsaverage description: | - 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]). + The `fsaverage` is a surface reference system + (formerly described as fsaverage\[3\|4\|5\|6\|sym\]). + Additionally, by convention, + `fsaverage` is used as shorthand for a **dual template** providing both volumetric and + surface coordinates references, + where the surface template is `fsaverage` and the volumetric template corresponds to a + FreeSurfer variant of `MNI305` space. Used by Freesurfer. fsaverageSym: value: fsaverageSym display_name: fsaverageSym description: | - 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 `fsaverageSym` atlas also defines a symmetric surface reference system + The `fsaverageSym` is a symmetric surface reference system (formerly described as `fsaveragesym`). + Additionally, by convention, + `fsaverageSym` is used as shorthand for a **dual template** providing both volumetric and + surface coordinates references, + where the surface template is `fsaverageSym` and the volumetric template corresponds to a + FreeSurfer variant of `MNI305` space. Used by Freesurfer. fsLR: value: fsLR display_name: fsLR description: | - The `fsLR` is a **dual template** providing both volumetric and surface coordinates references. - The volumetric template corresponds to `MNI152NLin6Asym`. + The `fsLR` is a surface template. + Additionally, by convention, + `fsLR` is used as shorthand for a **dual template** providing both volumetric and surface + coordinates references, + where the surface template is `fsLR` and the volumetric template corresponds 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. - Used by Freesurfer. + Used by Freesurfer and Connectome Workbench. MNIColin27: value: MNIColin27 display_name: MNIColin27