From 6476b0bdd45565d2e583b57f7cfa955241662f8a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Tue, 23 Jun 2020 13:58:00 -0400
Subject: [PATCH] Import structural derivatives from gh-207

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 create mode 100644 src/05-derivatives/04-structural-derivatives.md

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+# Structural (anatomical) derivatives
+
+## Reconstructed cortical surfaces
+
+Reconstructed cortical surfaces should be stored as GIFTI files, and each
+hemisphere should be stored separately.
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        anat/
+            <source_keywords>_hemi-{L|R}[_space-<surfspace>][_volspace-<volspace>][_desc-<label>]_<surftype>.surf.gii
+```
+
+Example:
+
+```Text
+pipeline/
+    sub-001/
+        anat/
+            sub-001_hemi-L_pial.surf.gii
+            sub-001_hemi-R_pial.surf.gii
+```
+
+The supported surface types (`<surftype>` suffix) are:
+
+| `<surftype>` | Description                                                          |
+| ------------ | -------------------------------------------------------------------- |
+| wm           | The gray matter / white matter border for the cortex                 |
+| smoothwm     | The smoothed gray matter / white matter border                       |
+| pial         | The gray matter / pial matter border                                 |
+| midthickness | The midpoints between wm and pial surfaces                           |
+| inflated     | An inflation of the midthickness surface (useful for visualization)  |
+| vinflated    | A very-inflated midthicknesss surface (also for visualization)       |
+| sphere       | The sphere (used for registration - see transforms for nomenclature) |
+| flat         | The flattened surface (used for visualization)                       |
+
+`space` filename keyword is restricted to
+[Surface Coordinate Spaces](../99-appendices/08-coordinate-systems.md#Surface)
+and `volspace` corresponds to the 3D coordinate space described in
+[Volume Coordinate Spaces](../99-appendices/08-coordinate-systems.md#Volume). In
+contrast to other derivatives the sidecar metadata field `SpatialReference` (see
+[Introduction](01-introduction.md#Common-file-level-metadata-fields)) is not
+required for any space, but is recommended when `volspace` is set to
+`individual`. In such case it should point to the volume defining the 3D
+coordinate system with witch the surface mesh is aligned with.
+
+## Surface-Mapped Anatomical Scalar Derivatives
+
+Surface-mapped scalar overlays should be stored as either GIFTI or CIFTI files
+(which allow for the combination of left and right hemispheres).
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        anat/
+            <source_keywords>[_hemi-{L|R}][_space-<space>][_desc-<label>]_<suffix>.{shape.gii|dscalar.nii}
+```
+
+The REQUIRED extension for scalar GIFTI files is `.shape.gii`. The `hemi` key is
+required for GIFTI files. For example:
+
+```Text
+pipeline/
+    sub-001/
+        anat/
+            sub-001_hemi-L_curv.shape.gii
+            sub-001_hemi-R_curv.shape.gii
+```
+
+The REQUIRED extension for scalar CIFTI files is `.dscalar.nii`. For example:
+
+```Text
+pipeline/
+    sub-001/
+        anat/
+            sub-001_curv.dscalar.nii
+```
+
+The file `<suffix>` MUST be one of the following values:
+
+| `<suffix>`   | Description                                           |
+| ------------ | ----------------------------------------------------- |
+| `curv`       | Cortical surface curvature indices                    |
+| `thickness`  | Cortical thickness                                    |
+| `area`       | Discretized surface area across regions               |
+| `dist`       | Distance from a point                                 |
+| `defects`    | Marked regions with surface defects                   |
+| `sulc`       | Sulcal depth                                          |
+| `myelinmap`  | Myelin map calculated from T1w to T2w ratio           |
+| `distortion` | Distortion map calculated from a surface registration |
+
+## Morphometrics
+
+Structural statistics produced by segmentation routines should be stored within
+tsv files, which could contain common parameters specified in the table below.
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        func|anat|dwi/
+            <source_keywords>[_desc-<label>]_morph.tsv
+
+```
+
+Example:
+
+```Text
+pipeline/
+    sub-001/
+        anat/
+            sub-001_desc-volumetric_morph.tsv
+```
+
+| Column name | Description                                     |
+| ----------- | ----------------------------------------------- |
+| index       | RECOMMENDED. Label integer index                |
+| name        | RECOMMENDED. Structure name                     |
+| centroid    | OPTIONAL. Center coordinate of structure        |
+| volume      | OPTIONAL. Volume of structure                   |
+| intensity   | OPTIONAL. Intensity of voxels within structure  |
+| thickness   | OPTIONAL. Thickness of cortical structure       |
+| area        | OPTIONAL. Surface area of cortical structure    |
+| curv        | OPTIONAL. Curvature index of cortical structure |
+
+Some parameters might require unit specification or have multiple associated
+statistics (such as avg, std, min, max, range). The suggested syntax for such
+columns is `<parameter>[-<stat>][-<units>]`. An example volumetric stats file
+might look something like this:
+
+```Text
+index  name               volume-mm3  intensity-avg  intensity-std
+11     Brainstem          23415.9     80.11          3.40
+32     Left-Hippocampus   5349.7      75.23          2.27
+32     Right-Hippocampus  4112.1      76.98          4.01
+```