From 0be3b9b42c2fe8775c4e693963aede653f598699 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 15 Aug 2019 12:10:24 -0700 Subject: [PATCH 01/18] [FIX] Normalization of template-generated standard spaces Unfolded from #213. I'm splitting that PR into two: one here to the current spec, sorting out existing templates; and a second to the `common-derivatives` branch to make it consistent with this one and adding my suggestions regarding spaces. --- src/99-appendices/08-coordinate-systems.md | 46 ++++++++++++++-------- 1 file changed, 30 insertions(+), 16 deletions(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index 756d2c9ec8..f4701a1ece 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -112,21 +112,35 @@ 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. -| Coordinate System | Description | -| --------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| 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) | -| 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 | [http://mindboggle.info/data.html](http://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/) | -| 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 | -| 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) | +### 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\[3|4|5|6|sym\] | (DISCOURAGED, 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]`). | +| 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`). | +| 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. | +| 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) | +| 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) | +| 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) | +| 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. See [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) | +| UNCInfant\[0|1|2\]V\[21|22|23\] | DISCOURAGED, please use ``UNCInfant`` without modifiers. 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`. | +| study | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. | --- From 352188cc484b496c44f709a10b5580fb1c9fc868 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 15 Aug 2019 12:17:16 -0700 Subject: [PATCH 02/18] fix: removed some items that sneaked in from #230 --- src/99-appendices/08-coordinate-systems.md | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index f4701a1ece..764316e4eb 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -122,7 +122,6 @@ the units are assumed to be mm. | fsaverage\[3|4|5|6|sym\] | (DISCOURAGED, 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]`). | | 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`). | -| 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. | | 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) | | 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) | @@ -136,11 +135,4 @@ the units are assumed to be mm. | UNCInfant | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | | UNCInfant\[0|1|2\]V\[21|22|23\] | DISCOURAGED, please use ``UNCInfant`` without modifiers. 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`. | -| study | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. | - --- From 3dfea45ece1257a5451803a6618f98052a093fff Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 15 Aug 2019 15:33:06 -0700 Subject: [PATCH 03/18] fix: mindboggle links --- src/99-appendices/08-coordinate-systems.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index 764316e4eb..b6a2461e1a 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -130,7 +130,7 @@ the units are assumed to be mm. | 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) | +| 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://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) | | UNCInfant\[0|1|2\]V\[21|22|23\] | DISCOURAGED, please use ``UNCInfant`` without modifiers. Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | From aec4090909380291218873176dd4f021deb628ee Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 15 Aug 2019 15:39:16 -0700 Subject: [PATCH 04/18] fix: minor revision of fsaverages --- src/99-appendices/08-coordinate-systems.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index b6a2461e1a..d5d039ddae 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -119,8 +119,8 @@ 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/) | -| fsaverage\[3|4|5|6|sym\] | (DISCOURAGED, 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]`). | +| fsaverage\[3|4|5|6|sym\] | DISCOURAGED, please use `fsaverage` without modifiers. 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\[3|4|5|6|sym\]). | | 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`). | | 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) | From 2d0eedd7ee66ed9819e743ff92033c19c3777363 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 15 Aug 2019 15:50:02 -0700 Subject: [PATCH 05/18] fix: outdated LONI links to atlases --- src/99-appendices/08-coordinate-systems.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index d5d039ddae..011020af8c 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -116,8 +116,8 @@ the units are assumed to be mm. | 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) | +| 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.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) | | fsaverage\[3|4|5|6|sym\] | DISCOURAGED, please use `fsaverage` without modifiers. 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\[3|4|5|6|sym\]). | From 96d212e40f84b52fe64af588be7e41189083bd07 Mon Sep 17 00:00:00 2001 From: oesteban Date: Thu, 15 Aug 2019 16:09:44 -0700 Subject: [PATCH 06/18] enh: add ``fsLR`` --- src/99-appendices/08-coordinate-systems.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index 011020af8c..04d7d139a0 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -122,6 +122,7 @@ the units are assumed to be mm. | fsaverage\[3|4|5|6|sym\] | DISCOURAGED, please use `fsaverage` without modifiers. 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\[3|4|5|6|sym\]). | | 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`). | +| 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. | | 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) | | 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) | From c8faa5938b1db4df1e7ec9278158b5154530d96e Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 30 Aug 2019 15:11:50 -0700 Subject: [PATCH 07/18] fix: address @satra's latest comments --- src/99-appendices/08-coordinate-systems.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index 04d7d139a0..fede546773 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -120,16 +120,15 @@ the units are assumed to be mm. | 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.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) | | fsaverage\[3|4|5|6|sym\] | DISCOURAGED, please use `fsaverage` without modifiers. 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\[3|4|5|6|sym\]). | -| 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`). | +| fsaverage\[3|Sym\] | 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 `fsaverageSym` is the symmetric counterpart of `fsaverage`. | | 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. | | 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) | | 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) | | 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) | -| 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. See [10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024). | +| 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. See [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) | +| NIHPD\[Sym|Asym\] | 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 | [https://mindboggle.info/data.html](https://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/) | From 48cb1bee0c6efc05d0b12ad313278341fc0e0c94 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Fri, 6 Sep 2019 12:28:14 -0700 Subject: [PATCH 08/18] Update src/99-appendices/08-coordinate-systems.md Co-Authored-By: Chris Markiewicz --- src/99-appendices/08-coordinate-systems.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index fede546773..c245f4cefe 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -133,6 +133,6 @@ the units are assumed to be mm. | 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://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) | -| UNCInfant\[0|1|2\]V\[21|22|23\] | DISCOURAGED, please use ``UNCInfant`` without modifiers. Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | +| UNCInfant\[0|1|2\]V\[21|22|23\] | DISCOURAGED, please use `UNCInfant` without modifiers. Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | --- From 5618813e3ae3e61ddb851b08beb8185d9e0e455e Mon Sep 17 00:00:00 2001 From: oesteban Date: Fri, 6 Sep 2019 12:35:57 -0700 Subject: [PATCH 09/18] fix: split discouraged identifiers, as per suggestion from @effigies --- src/99-appendices/08-coordinate-systems.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index c245f4cefe..43ffcd03df 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -119,8 +119,7 @@ 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" [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.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) | -| fsaverage\[3|4|5|6|sym\] | DISCOURAGED, please use `fsaverage` without modifiers. Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template | -| fsaverage\[3|Sym\] | 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 `fsaverageSym` is the symmetric counterpart of `fsaverage`. | +| fsaverage\[|Sym\] | 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 `fsaverageSym` is the symmetric counterpart of `fsaverage`. | | 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. | | 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) | @@ -133,6 +132,15 @@ the units are assumed to be mm. | 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://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) | -| UNCInfant\[0|1|2\]V\[21|22|23\] | DISCOURAGED, please use `UNCInfant` without modifiers. 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. +Their use is NOT RECOMMENDED for new BIDS datasets and tooling, but their +presence MUST NOT produce a validation error. + +| Coordinate System | Recommended identifier | +| --------------------------------------------------- | ---------------------- | +| fsaverage\[3|4|5|6|sym\] | fsaverage\[|Sym\] | +| UNCInfant\[0|1|2\]V\[21|22|23\] | UNCInfant | --- From 5a00a6b2439ee53004ee379c8b9fad36f0b0d280 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Fri, 6 Sep 2019 14:44:41 -0700 Subject: [PATCH 10/18] Update src/99-appendices/08-coordinate-systems.md Co-Authored-By: Chris Markiewicz --- src/99-appendices/08-coordinate-systems.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index 43ffcd03df..79ecdbed0e 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -118,7 +118,7 @@ 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" [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.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) | +| 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\[|Sym\] | 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 `fsaverageSym` is the symmetric counterpart of `fsaverage`. | | 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. | | 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) | From 73562390274cd33734ed5f56fb4e85a1c738a43f Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 4 Sep 2019 15:10:12 +0200 Subject: [PATCH 11/18] add software filters to EEG json example --- src/04-modality-specific-files/03-electroencephalography.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md index ae1620de1e..aee66e93b7 100644 --- a/src/04-modality-specific-files/03-electroencephalography.md +++ b/src/04-modality-specific-files/03-electroencephalography.md @@ -163,6 +163,12 @@ Example: "EEGPlacementScheme":"10 percent system", "EEGReference":"single electrode placed on FCz", "EEGGround":"placed on AFz", + "SoftwareFilters":{ + "Anti-aliasing filter":{ + "half-amplitude cutoff (Hz)": 500, + "Roll-off": "6dB/Octave" + } + }, "HardwareFilters":{ "ADC's decimation filter (hardware bandwidth limit)":{ "-3dB cutoff point (Hz)":480, From b7be97b5c3f830fc54a58683380b348694f38a01 Mon Sep 17 00:00:00 2001 From: Changelog-bot Date: Fri, 11 Oct 2019 12:02:23 +0000 Subject: [PATCH 12/18] [DOC] Auto-generate changelog entry for PR #322 --- src/CHANGES.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/CHANGES.md b/src/CHANGES.md index 7e33a5d03b..e8236b41c1 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -4,11 +4,13 @@ Changelog - \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold)) +- ENH: Clarify the position toward non-compliant derivative datasets and files [#334](https://github.com/bids-standard/bids-specification/pull/334) ([effigies](https://github.com/effigies)) - \[ENH] Clarify phenotypic and assessment data in new section [#331](https://github.com/bids-standard/bids-specification/pull/331) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] add information about continuous integration checks to PR template [#330](https://github.com/bids-standard/bids-specification/pull/330) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Fix `Common principles` `Key/value files` section level [#328](https://github.com/bids-standard/bids-specification/pull/328) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Set the maximum heading length lint check to `false` [#325](https://github.com/bids-standard/bids-specification/pull/325) ([jhlegarreta](https://github.com/jhlegarreta)) - \[FIX] Number explicitly all cases in MRI field map section headers [#323](https://github.com/bids-standard/bids-specification/pull/323) ([jhlegarreta](https://github.com/jhlegarreta)) +- \[FIX] Add SoftwareFilters to EEG sidecar example [#322](https://github.com/bids-standard/bids-specification/pull/322) ([Remi-Gau](https://github.com/Remi-Gau)) - \[MISC] Fixing Travis errors with Remark [#320](https://github.com/bids-standard/bids-specification/pull/320) ([franklin-feingold](https://github.com/franklin-feingold)) - \[INFRA] Link to doc builds in CI checks [#315](https://github.com/bids-standard/bids-specification/pull/315) ([jasmainak](https://github.com/jasmainak)) - \[MISC] Add BEP027 - BIDS Execution to BEP list [#314](https://github.com/bids-standard/bids-specification/pull/314) ([effigies](https://github.com/effigies)) From 26ff2e0e0905bf26b2fc976ab57b57909c73dd94 Mon Sep 17 00:00:00 2001 From: Sam Nastase Date: Mon, 14 Oct 2019 01:56:52 -0400 Subject: [PATCH 13/18] Typo fix (contract -> contrast) in events documentation --- src/04-modality-specific-files/05-task-events.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/04-modality-specific-files/05-task-events.md b/src/04-modality-specific-files/05-task-events.md index 35a9e751ec..5d35a72040 100644 --- a/src/04-modality-specific-files/05-task-events.md +++ b/src/04-modality-specific-files/05-task-events.md @@ -20,7 +20,7 @@ recorded during the scan. Events MAY be either stimuli presented to the participant or participant responses. A single event file MAY include any combination of stimuli and response events. Events MAY overlap in time. Please mind that this does not imply that only so called "event related" study designs -are supported (in contract to "block" designs) - each "block of events" can be +are supported (in contrast to "block" designs) - each "block of events" can be represented by an individual row in the \_events.tsv file (with a long duration). Each task events file REQUIRES a corresponding task imaging data file (but a single events file MAY be shared by multiple imaging data files - see From c6037c563cd1a6a454fcd835f19cf34f33e8f1b4 Mon Sep 17 00:00:00 2001 From: Changelog-bot Date: Tue, 15 Oct 2019 08:26:53 +0000 Subject: [PATCH 14/18] [DOC] Auto-generate changelog entry for PR #346 --- src/CHANGES.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/CHANGES.md b/src/CHANGES.md index e8236b41c1..ff62092f0c 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,6 +2,7 @@ Changelog ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) +- \[FIX] Typo fix (contract -> contrast) in events documentation [#346](https://github.com/bids-standard/bids-specification/pull/346) ([snastase](https://github.com/snastase)) - \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold)) - ENH: Clarify the position toward non-compliant derivative datasets and files [#334](https://github.com/bids-standard/bids-specification/pull/334) ([effigies](https://github.com/effigies)) From 84be32ad8b5e0e0f55c3720151141449b5edd423 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Wed, 16 Oct 2019 12:39:40 +0200 Subject: [PATCH 15/18] clarify that filters should be specified as object of objects --- .../02-magnetoencephalography.md | 58 +++++++++---------- .../03-electroencephalography.md | 48 +++++++-------- .../04-intracranial-electroencephalography.md | 46 +++++++-------- 3 files changed, 76 insertions(+), 76 deletions(-) diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index e4b594cec6..a70c6e4b4e 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -81,38 +81,38 @@ Whenever possible, please avoid using ad-hoc wording. Specific MEG fields MUST be present: -| Field name | Definition | -| :------------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | -| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | -| SoftwareFilters | REQUIRED. List of temporal and/or spatial software filters applied, or ideally key:value pairs of pre-applied software filters and their parameter values: e.g., {"SSS": {"frame": "head", "badlimit": 7}}, {"SpatialCompensation": {"GradientOrder": Order of the gradient compensation}}. Write `n/a` if no software filters applied. | -| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | -| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | +| Field name | Definition | +| :------------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | +| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"SSS": {"frame": "head", "badlimit": 7}, "SpatialCompensation": {"GradientOrder": "Order of the gradient compensation"}} | +| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | +| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | SHOULD be present -| Field name | Definition | -| :------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) | -| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 | -| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) | -| ECOGChannelCount | RECOMMENDED. Number of ECoG channels | -| SEEGChannelCount | RECOMMENDED. Number of SEEG channels | -| EOGChannelCount | RECOMMENDED. Number of EOG channels | -| ECGChannelCount | RECOMMENDED. Number of ECG channels | -| EMGChannelCount | RECOMMENDED. Number of EMG channels | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) | -| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data | -| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. | -| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in BTi/4D) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) | -| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) | -| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | -| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). | -| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. | +| Field name | Definition | +| :------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) | +| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 | +| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) | +| ECOGChannelCount | RECOMMENDED. Number of ECoG channels | +| SEEGChannelCount | RECOMMENDED. Number of SEEG channels | +| EOGChannelCount | RECOMMENDED. Number of EOG channels | +| ECGChannelCount | RECOMMENDED. Number of ECG channels | +| EMGChannelCount | RECOMMENDED. Number of EMG channels | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) | +| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data | +| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. | +| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in BTi/4D) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) | +| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) | +| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | +| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). | +| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | Specific EEG fields (if recorded with MEG) SHOULD be present: diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md index aee66e93b7..71cb1adb01 100644 --- a/src/04-modality-specific-files/03-electroencephalography.md +++ b/src/04-modality-specific-files/03-electroencephalography.md @@ -112,33 +112,33 @@ Whenever possible, please avoid using ad hoc wording. Specific EEG fields MUST be present: -| Field name | Definition | -| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). | -| SoftwareFilters | REQUIRED. List of temporal software filters applied. Ideally key:value pairs of pre-applied software filters and their parameter values: e.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. Write `n/a` if no software filters applied. | +| Field name | Definition | +| :----------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. | SHOULD be present: -| Field name | Definition | -| :--------------------------| :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). | -| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). | -| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). | -| ECGChannelCount | RECOMMENDED. Number of ECG channels. | -| EMGChannelCount | RECOMMENDED. Number of EMG channels. | -| EOGChannelCount | RECOMMENDED. Number of EOG channels. | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | -| RecordingType | RECOMMENDED. Defines whether the recording is `continuous`, `discontinuous` or `epoched`. | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. | -| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). | -| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). | -| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). | -| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. | -| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | +| Field name | Definition | +| :--------------------------| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). | +| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). | +| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). | +| ECGChannelCount | RECOMMENDED. Number of ECG channels. | +| EMGChannelCount | RECOMMENDED. Number of EMG channels. | +| EOGChannelCount | RECOMMENDED. Number of EOG channels. | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | +| RecordingType | RECOMMENDED. Defines whether the recording is `continuous`, `discontinuous` or `epoched`. | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. | +| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). | +| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). | +| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). | +| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | Example: diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md index d5b070820a..9385322ca2 100644 --- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md +++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md @@ -66,7 +66,7 @@ in the sidecar JSON file. Other relevant files MAY be included alongside the original iEEG data in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data). Note the RecordingType, which depends on whether the data stream on disk is interrupted or not. Continuous data is by definition 1 segment without interruption. Epoched data consists of multiple segments that all have the same length (e.g., corresponding to trials) and that have gaps in between. Discontinuous data consists of multiple segments of different length, for example due to a pause in the acquisition. - + ### Terminology: Electrodes vs. Channels For proper documentation of iEEG recording metadata it is important to @@ -130,31 +130,31 @@ Specific iEEG fields MUST be present: | iEEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "bipolar", "T01" for electrode with name T01, "intracranial electrode on top of a grid, not included with data", "upside down electrode"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | | SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the iEEG channels in the recording (e.g., 2400). All other channels should have frequency specified as well in the `channels.tsv` file. | | PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid where the iEEG recording was done (i.e., 50 or 60). | -| SoftwareFilters | REQUIRED. List of temporal software filters applied or ideally key:value pairs of pre-applied filters and their parameter values. (n/a if none). E.g., "{'HighPass': {'HalfAmplitudeCutOffHz': 1, 'RollOff: '6dB/Octave'}}". | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"HighPass": {"HalfAmplitudeCutOffHz": 1, "RollOff": "6dB/Octave"}}` | Specific iEEG fields SHOULD be present: -| Field name | Definition | -| :------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". | -| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. | -| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. | -| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. | -| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). | -| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). | -| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). | -| EOGChannelCount | RECOMMENDED. Number of EOG channels. | -| ECGChannelCount | RECOMMENDED. Number of ECG channels. | -| EMGChannelCount | RECOMMENDED. Number of EMG channels. | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | -| RecordingType | RECOMMENDED. Defines whether the recording is "continuous", "discontinuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. | -| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). | -| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). | -| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. | -| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. | +| Field name | Definition | +| :------------------------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". | +| HardwareFilters | RECOMMENDED.A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. | +| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. | +| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). | +| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). | +| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). | +| EOGChannelCount | RECOMMENDED. Number of EOG channels. | +| ECGChannelCount | RECOMMENDED. Number of ECG channels. | +| EMGChannelCount | RECOMMENDED. Number of EMG channels. | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | +| RecordingType | RECOMMENDED. Defines whether the recording is "continuous", "discontinuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. | +| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). | +| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). | +| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. | +| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. | Specific iEEG fields MAY be present: From e7ddb6490c2a48da72eee62206d19fd5fdfaa9f7 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Wed, 16 Oct 2019 14:14:38 +0200 Subject: [PATCH 16/18] add missing code specifier --- .../02-magnetoencephalography.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index a70c6e4b4e..e8e68c1b7d 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -81,14 +81,14 @@ Whenever possible, please avoid using ad-hoc wording. Specific MEG fields MUST be present: -| Field name | Definition | -| :------------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | -| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | -| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"SSS": {"frame": "head", "badlimit": 7}, "SpatialCompensation": {"GradientOrder": "Order of the gradient compensation"}} | -| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | -| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | +| Field name | Definition | +| :------------------ | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | +| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"SSS": {"frame": "head", "badlimit": 7}, "SpatialCompensation": {"GradientOrder": "Order of the gradient compensation"}}` | +| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | +| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | SHOULD be present From 3690b884286f34c9f0128f5d87f79967c61762bd Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Fri, 18 Oct 2019 12:28:11 +0200 Subject: [PATCH 17/18] address code review by @jasmainak --- .../02-magnetoencephalography.md | 58 +++++++++---------- .../03-electroencephalography.md | 48 +++++++-------- .../04-intracranial-electroencephalography.md | 44 +++++++------- 3 files changed, 75 insertions(+), 75 deletions(-) diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index e8e68c1b7d..50acb4fb08 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -81,38 +81,38 @@ Whenever possible, please avoid using ad-hoc wording. Specific MEG fields MUST be present: -| Field name | Definition | -| :------------------ | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | -| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | -| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"SSS": {"frame": "head", "badlimit": 7}, "SpatialCompensation": {"GradientOrder": "Order of the gradient compensation"}}` | -| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | -| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | +| Field name | Definition | +| :------------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | +| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"SSS": {"frame": "head", "badlimit": 7}, "SpatialCompensation": {"GradientOrder": "Order of the gradient compensation"}}` | +| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | +| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | SHOULD be present -| Field name | Definition | -| :------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) | -| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 | -| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) | -| ECOGChannelCount | RECOMMENDED. Number of ECoG channels | -| SEEGChannelCount | RECOMMENDED. Number of SEEG channels | -| EOGChannelCount | RECOMMENDED. Number of EOG channels | -| ECGChannelCount | RECOMMENDED. Number of ECG channels | -| EMGChannelCount | RECOMMENDED. Number of EMG channels | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) | -| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data | -| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. | -| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in BTi/4D) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) | -| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) | -| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | -| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). | -| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| Field name | Definition | +| :------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) | +| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 | +| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) | +| ECOGChannelCount | RECOMMENDED. Number of ECoG channels | +| SEEGChannelCount | RECOMMENDED. Number of SEEG channels | +| EOGChannelCount | RECOMMENDED. Number of EOG channels | +| ECGChannelCount | RECOMMENDED. Number of ECG channels | +| EMGChannelCount | RECOMMENDED. Number of EMG channels | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) | +| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data | +| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. | +| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in BTi/4D) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) | +| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) | +| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | +| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). | +| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | Specific EEG fields (if recorded with MEG) SHOULD be present: diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md index 71cb1adb01..02f90cabae 100644 --- a/src/04-modality-specific-files/03-electroencephalography.md +++ b/src/04-modality-specific-files/03-electroencephalography.md @@ -112,33 +112,33 @@ Whenever possible, please avoid using ad hoc wording. Specific EEG fields MUST be present: -| Field name | Definition | -| :----------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). | -| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. | +| Field name | Definition | +| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. | SHOULD be present: -| Field name | Definition | -| :--------------------------| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). | -| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). | -| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). | -| ECGChannelCount | RECOMMENDED. Number of ECG channels. | -| EMGChannelCount | RECOMMENDED. Number of EMG channels. | -| EOGChannelCount | RECOMMENDED. Number of EOG channels. | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | -| RecordingType | RECOMMENDED. Defines whether the recording is `continuous`, `discontinuous` or `epoched`. | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. | -| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). | -| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). | -| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). | -| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | -| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | +| Field name | Definition | +| :--------------------------| :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). | +| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). | +| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). | +| ECGChannelCount | RECOMMENDED. Number of ECG channels. | +| EMGChannelCount | RECOMMENDED. Number of EMG channels. | +| EOGChannelCount | RECOMMENDED. Number of EOG channels. | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | +| RecordingType | RECOMMENDED. Defines whether the recording is `continuous`, `discontinuous` or `epoched`. | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. | +| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). | +| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). | +| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). | +| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | Example: diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md index 9385322ca2..267e5824b1 100644 --- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md +++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md @@ -130,31 +130,31 @@ Specific iEEG fields MUST be present: | iEEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "bipolar", "T01" for electrode with name T01, "intracranial electrode on top of a grid, not included with data", "upside down electrode"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | | SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the iEEG channels in the recording (e.g., 2400). All other channels should have frequency specified as well in the `channels.tsv` file. | | PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid where the iEEG recording was done (i.e., 50 or 60). | -| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"HighPass": {"HalfAmplitudeCutOffHz": 1, "RollOff": "6dB/Octave"}}` | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"HighPass": {"HalfAmplitudeCutOffHz": 1, "RollOff": "6dB/Octave"}}` | Specific iEEG fields SHOULD be present: -| Field name | Definition | -| :------------------------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". | -| HardwareFilters | RECOMMENDED.A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available of applicable. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | -| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. | -| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. | -| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). | -| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). | -| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). | -| EOGChannelCount | RECOMMENDED. Number of EOG channels. | -| ECGChannelCount | RECOMMENDED. Number of ECG channels. | -| EMGChannelCount | RECOMMENDED. Number of EMG channels. | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | -| RecordingType | RECOMMENDED. Defines whether the recording is "continuous", "discontinuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. | -| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). | -| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). | -| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. | -| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. | +| Field name | Definition | +| :------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". | +| HardwareFilters | RECOMMENDED.A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. | +| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. | +| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). | +| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). | +| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). | +| EOGChannelCount | RECOMMENDED. Number of EOG channels. | +| ECGChannelCount | RECOMMENDED. Number of ECG channels. | +| EMGChannelCount | RECOMMENDED. Number of EMG channels. | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | +| RecordingType | RECOMMENDED. Defines whether the recording is "continuous", "discontinuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. | +| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). | +| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). | +| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. | +| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. | Specific iEEG fields MAY be present: From 264e1b210b82614aaf3881af156c503ab61f038b Mon Sep 17 00:00:00 2001 From: Changelog-bot Date: Wed, 30 Oct 2019 13:33:09 +0000 Subject: [PATCH 18/18] [DOC] Auto-generate changelog entry for PR #348 --- src/CHANGES.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/CHANGES.md b/src/CHANGES.md index ff62092f0c..05c197e47b 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,6 +2,8 @@ Changelog ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) +- specify further the pipeline following #345 [#358](https://github.com/bids-standard/bids-specification/pull/358) ([CPernet](https://github.com/CPernet)) +- FIX: clarify that filters should be specified as object of objects [#348](https://github.com/bids-standard/bids-specification/pull/348) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Typo fix (contract -> contrast) in events documentation [#346](https://github.com/bids-standard/bids-specification/pull/346) ([snastase](https://github.com/snastase)) - \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold))