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Merge pull request #5 from chrisfilo/enh/cifti_spaces
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[ENH] Adding hybrid spaces for CIFTI use
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@chrisgorgo
chrisgorgo authored Mar 7, 2019
2 parents 78a9350 + 132cb3e commit 100432a
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22 changes: 19 additions & 3 deletions src/99-appendices/08-coordinate-systems.md
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Expand Up @@ -158,6 +158,8 @@ 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.

### Volume

| Coordinate System | Description |
| --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| FS305 | FreeSurfer variant of the MNI305 space |
Expand All @@ -174,9 +176,23 @@ the units are assumed to be mm.
| 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/) |
| fsnative | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image |
| 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\[164k|32k\] | Images were sampled to the 164k or 32k fsaverage_LR surface reconstructed from the T1w image (high resolution space of the HCPPipelines) |
| 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 |
| -------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| fsnative | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image |
| 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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