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@@ -53,6 +53,24 @@ This repository contains multi-channel spatio-temporal MRI atlas of normal fetal
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- the multi-label brain tissue parcellation protocol was formalised based on both research relevance and visibility of individual structures in T2w images; it has 19 ROIs with separate R/L structures defined based on the fetal brain histology atlases (Bayer et al., 2003; Bayer et al., 2005); the parcellation map was created using a combination of semi-manual refinement of the optimised dHCP DRAW-Em neonatal pipeline segmentations [(Makropoulos et al., 2018)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783314/) and registration between the atlas time-points
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+-----
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+### Comments
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+
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+- to transform the atlas timepoints to the world space (all timepoints are currently affinely scaled to the same space) - please use the following MIRTK command using affine transforms from the "transformations folder":
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+
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+```bash
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+ga=24
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+mirtk transform-image t2-t${ga}.00.nii.gz transformed-t2-t${ga}.00.nii.gz -dofin affine-${ga}.dof -interp BSpline -target t2-t36.00.nii.gz
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+```
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+
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+- to visualise atlas channels including ODF - please use the following MRtrix3 command:
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+
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+```bash
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+ga=24
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+mrview t2-t${ga}.00.nii.gz t1-t${ga}.00.nii.gz fa-t${ga}.00.nii.gz -odf.load_sh odf-t${ga}.00.nii.gz
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+```
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+
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+
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-----
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### License
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