Browse Source

Initial import of atlas files

Andreas Schuh 4 years ago
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LICENSE.md

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+[![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)][license]
+
+# Morphological atlas of neonatal brain development
+
+<div align="center">
+  <img src="figures/overview.png" alt="Atlas images" width="90%"/>
+</div>
+
+Spatio-temporal neonatal brain atlas constructed as part of the [Developing Human Connectome Project (dHCP)][dhcp].
+The methodology used to built this temporally consistent atlas was first presented in [Schuh, 2017][Schuh2017-hdl] and [Schuh *et al.*, 2018][Schuh2018-doi].
+
+*For a cortical surface atlas following a related but different approach [(Bozek et al., 2018)][Bozek2018-doi],
+follow [this link][surface-atlas].*
+
+
+## Content
+
+Directory                 | Description
+:-------------------------|:----------------------------------------------------------------------------------
+[config](config/)         | Configuration files with [parameters](config/params.json) used to build the atlas and [ages](config/sessions.csv) of the neonates.
+[figures](figures/)       | Images of figures displayed in this README file.
+[global](global/)         | Affine transformations used to globally normalise the input brain images.
+[mean](mean/)             | Contains the mean intensity images and hard segmentations for gestational age 36 to 44 weeks.
+[structures](structures/) | Posterior probability maps of the [87 brain structures](config/structures.txt) for each atlas time point.
+[tissues](tissues/)       | Posterior probability maps of the [9 tissue classes](config/tissues.txt) for each atlas time point.
+[scale](scale/)           | Regressed anisotropic global scaling of each atlas time point.
+
+The following image files are located underneath the age-specific directories (`ga_{36..44}`) of the `mean` folder:
+
+Image file           | Description
+:--------------------|:---------------------------------------------------------------------------
+`mask.nii.gz`        | Average brain extraction mask.
+`average_t1.nii.gz`  | Mean T1-weighted intensity image.
+`average_t2.nii.gz`  | Mean T2-weighted intensity image.
+`template_t1.nii.gz` | Mean T1-weighted intensity image after Laplacian sharpening.
+`template_t2.nii.gz` | Mean T2-weighted intensity image after Laplacian sharpening.
+`tissues.nii.gz`     | Hard tissue segmentation into [9 tissue classes](config/tissues.txt).
+`structures.nii.gz`  | Structural segmentation into [87 brain structures](config/structures.txt).
+
+It should be noted that all images are in a common global reference coordinate system. Therefore, the atlas images do not reflect global differences in average brain size between different atlas time points. The regressed anisotropic scaling factors for each atlas time point are provided. These can be applied to the images of the individual time points in order to create an image sequence which includes the global changes in brain size. How this can be done using the [MIRTK][mirtk], see [below](#software).
+
+*Note: The posterior maps of tissue classes and brain structures may be downloaded as separate archives.*
+
+
+## License
+
+This brain atlas is distributed under the terms of the [Creative Commons Attribution 4.0 International][license] license.
+<!-- See accompanying LICENSE.md file for details or follow the link given below. -->
+
+
+## Citation
+
+[Andreas Schuh][aschuh], [Antonios Makropoulos][amakropoulos], [Emma C. Robinson][erobinson], Lucilio Cordero-Grande, Emer Hughes, Jana Hutter, Anthony N. Price, Maria Murgasova, Rui Pedro A. G. Teixeira, Nora Tusor, Johannes Steinweg, Suresh Victor, Mary A. Rutherford, Joseph V. Hajnal, A. David Edwards, and [Daniel Rueckert][drueckert], **Unbiased construction of a temporally consistent morphological atlas of neonatal brain development**, *bioRxiv*, 2018. **doi:** [10.1101/251512][Schuh2018-doi]
+
+
+    @article {Schuh2018,
+      author = {Schuh, Andreas and Makropoulos, Antonios and Robinson, Emma C. and Cordero-Grande, Lucilio and Hughes, Emer and Hutter, Jana and Price, Anthony N and Murgasova, Maria and Teixeira, Rui Pedro A. G. and Tusor, Nora and Steinweg, Johannes K. and Victor, Suresh and Rutherford, Mary A. and Hajnal, Joseph V. and Edwards, A. David and Rueckert, Daniel},
+      title = {Unbiased construction of a temporally consistent morphological atlas of neonatal brain development},
+      journal = {bioRxiv},
+      year = {2018},
+      doi = {10.1101/251512},
+      publisher = {Cold Spring Harbor Laboratory}
+    }
+
+
+## Materials
+
+The used structural brain magnetic resonance images were collected at St. Thomas Hospital, London, UK, on a Philips 3T scanner using a dedicated 32 channel neonatal head coil as part of the [Developing Human Connectome Project (dHCP)][dhcp].
+
+T2-weighted images were obtained in two stacks of 2D slices using a Turbo Spin Echo (TSE) sequence using TR = 12 s, TE = 156 ms, SENSE factor 2.11 (axial) and 2.58 (sagittal). T1-weighted images were obtained using an Inversion Recovery TSE sequence with TR = 4.8 s, TE = 8.7 ms, SENSE factor 2.26 (axial) and 2.66 (sagittal). Images were acquired with overlapping slices at a resolution of 0.8 x 0.8 x 1.6 mm<sup>3</sup>. During motion corrected reconstruction, the images are resampled to an isotropic voxel size of 0.5 mm. Babies were imaged without sedation during natural sleep. The used images showed no structural abnormalities. Details of the image selection from in total 495 processed images are given in [Schuh *et al.*, 2018][Schuh2018-doi].
+
+The histograms below show the distribution of gestational age at birth (steps) and post-menstrual age at scan (bars) of the dataset consisting of 275 T1-weighted and T2-weighted brain images used to construct this spatio-temporal brain atlas.
+
+<div align="center">
+  <img src="figures/distribution.png" alt="Age distribution" width="480px"/>
+</div>
+
+
+## Methods
+
+All reconstructed volumes were preprocessed using a pipeline designed for neonatal brain images, including an initial rough brain extraction and bias field correction. The images were segmented into 87 regions of interest (ROIs) and 9 tissue classes (background, CSF, cGM, dGM, WM, ventricles, cerebellum, brainstem, hippocampi and amygdalae) using an extension of the [Developing Brain Region Annotation With Expectation-Maximization (Draw-EM)][drawem] algorithm. A detailed description of this pipeline is given in [Makropoulos *et al.*, 2018][Makropoulos2018-doi], and the [source code][Makropoulos2018-src] is available on GitHub.
+
+
+
+The spatio-temporal neonatal brain atlas construction is summarised in [Schuh *et al.*, 2018][Schuh2018-doi].
+
+<div align="center">
+  <img src="figures/construction.png" alt="Atlas construction" width="640px"/>
+</div>
+
+<div align="center">
+  <img src="figures/deformations.png" alt="Image deformations" width="480px"/>
+</div>
+
+Further details, including an evaluation of the employed diffeomorphic registration method, can be found in [Schuh, 2017][Schuh2017-hdl].
+
+
+## Software
+
+A software implementation in Python and C++ of the methodology used to built this spatio-temporal atlas is part of the [Medical Image Registration ToolKit (MIRTK)][mirtk], an open source image processing toolkit [available on GitHub][mirtk-web]. The parameters used for this software tool can be found in the [config/params.json](config/params.json) file. Specifically, we used [MIRTK v2.0][mirtk-v2.0].
+
+Given an installation of MIRTK, the atlas construction can be executed using the command:
+
+
+    mirtk construct-atlas config/params.json
+
+*Note: This requires additional input image files which are not distributed as part of this atlas. While not publicly available as of July 2018, the used reconstructed brain images and corresponding segmentations are expected to be released by the dHCP team at https://data.developingconnectome.org/.*
+
+An image sequence which includes the regressed average changes in brain size can be created, for example from the T2-weighted template images, using the following MIRTK commands executed on a Unix system in a [Bash shell](https://www.gnu.org/software/bash/manual/html_node/What-is-Bash_003f.html), where the current working directory is assumed to be set to the top-level directory of this atlas:
+
+    # Apply global scalings
+    mkdir -p temp
+    for t in {36..44}; do
+        mirtk transform-image mean/ga_$t/template_t2.nii.gz temp/template_t2_$t.nii.gz -dofin scale/ga_$t.dof -invert
+    done
+
+    # Combine 3D volumes into 3D+t image sequence
+    mirtk combine-images -images temp/template_t2_{36..44}.nii.gz -output seq.nii.gz
+
+    # Display image sequence using MIRTK viewer
+    mirtk view seq.nii.gz
+
+    # Delete output files (optional)
+    rm -f temp/template_t2_{36..44}.nii.gz
+    rmdir temp 2> /dev/null
+
+
+## Acknowledgements
+
+The work resulting in this brain atlas was done in the [Biomedical Image Analysis (BioMedIA)][biomedia] group at [Imperial College London][icl] as part of the [dHCP][dhcp], which received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) [grant #319456]. We are grateful to the families who generously supported this trial. The work was supported by the NIHR Biomedical Research Centers at Guy's and St Thomas' NHS Trust.
+
+
+## References
+
+
+*Data acquisition:*
+
+E. J. Hughes, T. Winchman, F. Padormo, R. Teixeira, J. Wurie, M. Sharma, M. Fox, J. Hutter, L. Cordero-Grande, A. N. Price, J. Allsop, J. Bueno-Conde, N. Tusor, T. Arichi, A. D. Edwards, M. A. Rutherford, S. J. Counsell, and J. V. Hajnal, **A dedicated neonatal brain imaging system**, *Magnetic Resonance in Medicine*, vol. 78 (2), pp. 794-804, 2017.
+[[abstract]][Hughes2016-doi] [[pdf]][Hughes2016-pdf]
+
+
+*Motion corrected reconstruction:*
+
+L. Cordero-Grande, E. J. Hughes, J. Hutter, A. N. Price, and J. V. Hajnal, **Three-dimensional motion corrected sensitivity encoding reconstruction for multi-shot multi-slice MRI: Application to neonatal brain imaging**, *Magnetic Resonance in Medicine*, vol. 79 (3), pp. 1365-76, 2018.
+[[abstract]][CorderoGrande2018-doi] [[pdf]][CorderoGrande2018-pdf]
+
+
+*Brain segmentation:*
+
+A. Makropoulos, E. C. Robinson, A. Schuh, R. Wright, S. Fitzgibbon, J. Bozek, S. J. Counsell, J. Steinweg, K. Vecchiato, J. Passerat-Palmbach, G. Lenz, F. Mortari, T. Tenev, E. P. Duff, M. Bastiani, L. Cordero-Grande, E. Hughes, N. Tusor, J.-D. Tournier, J. Hutter, A.N. Price, R. P. A. G. Teixeira, M. Murgasova, S. Victor, C. Kelly, M. A. Rutherford, S. M. Smith, A. D. Edwards, J. V. Hajnal, M. Jenkinson, D. Rueckert, **The developing human connectome project: A minimal processing pipeline for neonatal cortical surface reconstruction**, *NeuroImage*, vol. 173, pp. 88-112, 2018.
+[[abstract]][Makropoulos2018-doi] [[pdf]][Makropoulos2018-pdf] [[code]][Makropoulos2018-src]
+
+
+*Image registration and atlas construction:*
+
+A. Schuh, **Computational models of the morphology of the developing neonatal human brain**, *PhD thesis*, 2017.
+[[abstract]][Schuh2017-hdl] [[pdf]][Schuh2017-pdf]
+
+A. Schuh, A. Makropoulos, E. C. Robinson, L. Cordero-Grande, E. Hughes, J. Hutter, A. N. Price, M. Murgasova, R. P. A. G. Teixeira, N. Tusor, J. Steinweg, S. Victor, M. A. Rutherford, J. V. Hajnal, A. D. Edwards, and D. Rueckert, **Unbiased construction of a temporally consistent morphological atlas of neonatal brain development**, *bioRxiv*, preprint, 2018.
+[[abstract]][Schuh2018-doi] [[pdf]][Schuh2018-pdf] [[code]][Schuh2018-src]
+
+
+<!-- Links -->
+[license]: https://creativecommons.org/licenses/by/4.0/
+
+[aschuh]: http://andreasschuh.com/
+[amakropoulos]: http://antoniosmakropoulos.com/
+[erobinson]: https://emmarobinson01.com/
+[drueckert]: https://wp.doc.ic.ac.uk/dr/
+
+[biomedia]: https://biomedic.doc.ic.ac.uk
+[icl]: http://www.imperial.ac.uk/computing
+[dhcp]: http://www.developingconnectome.org/project/
+[surface-atlas]: https://brain-development.org/brain-atlases/cortical-surface-atlas/
+[drawem]: https://biomedia.doc.ic.ac.uk/software/draw-em/
+[mirtk]: https://biomedia.doc.ic.ac.uk/software/mirtk/
+[mirtk-web]: https://mirtk.github.io/
+[mirtk-v2.0]: https://github.com/BioMedIA/MIRTK/releases/tag/v2.0.0
+
+[Bozek2018-doi]: https://doi.org/10.1016/j.neuroimage.2018.06.018
+
+[Hughes2016-doi]: https://doi.org/10.1002/mrm.26462
+[Hughes2016-pdf]: https://onlinelibrary.wiley.com/doi/epdf/10.1002/mrm.26462
+
+[CorderoGrande2018-doi]: https://doi.org/10.1002/mrm.26796
+[CorderoGrande2018-pdf]: https://onlinelibrary.wiley.com/doi/epdf/10.1002/mrm.26796
+
+[Makropoulos2018-doi]: https://doi.org/10.1016/j.neuroimage.2018.01.054
+[Makropoulos2018-pdf]: https://www.biorxiv.org/content/early/2018/01/07/125526.full.pdf
+[Makropoulos2018-src]: https://github.com/BioMedIA/dhcp-structural-pipeline
+
+[Schuh2017-hdl]: http://hdl.handle.net/10044/1/58880
+[Schuh2017-pdf]: https://spiral.imperial.ac.uk/bitstream/10044/1/58880/1/Schuh-A-2018-PhD-Thesis.pdf
+
+[Schuh2018-doi]: https://doi.org/10.1101/251512
+[Schuh2018-pdf]: https://www.biorxiv.org/content/early/2018/01/28/251512.full.pdf
+[Schuh2018-src]: https://github.com/BioMedIA/MIRTK/releases/tag/v2.0.0

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BIN
config/domain.nii.gz


+ 129 - 0
config/params.json

@@ -0,0 +1,129 @@
+{
+    "paths": {
+        "topdir": "..",
+        "agecsv": "config/ages.csv",
+        "imgcsv": "config/subjects.csv",
+        "tmpdir": "cache",
+        "outdir": "output"
+    },
+    "images": {
+        "default": "t2w",
+        "ref": "config/domain.nii.gz",
+        "t1w": {
+            "prefix": "images/t1w/",
+            "suffix": ".nii.gz",
+            "interp": "linear",
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+        },
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+            "suffix": ".nii.gz",
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+            "rescaling": [1, 100],
+            "sharpen": true,
+            "bkgrnd": 0,
+            "bins": 0
+        },
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+            "prefix": "labels/tissues/",
+            "suffix": ".nii.gz",
+            "labels": "1..9",
+            "interp": "nn"
+        },
+        "structures": {
+            "prefix": "labels/structures/",
+            "suffix": ".nii.gz",
+            "labels": "1..87",
+            "interp": "nn"
+        }
+    },
+    "iterations": 8,
+    "registration": {
+        "affine": {
+            "prefix": "global/",
+            "suffix": ".dof"
+        },
+        "config": [
+            {
+                "energy": "Symmetric",
+                "model": "SVFFD",
+                "ffdim": "SS",
+                "intsteps": 64,
+                "liederiv": false,
+                "bchterms": 2,
+                "channels": ["t2w"],
+                "measures": {"t2w": "NMI"},
+                "padding": true,
+                "interpolation": "Linear with padding",
+                "foreground": "Union",
+                "levels": 3,
+                "resolution": 1.0,
+                "spacing": [8.0, 16.0, 32.0],
+                "bending": 1e-3,
+                "jacobian": 0e-0,
+                "blurring": {"tissues": 2, "structures": 2}
+            },
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+                "spacing": [8.0, 8.0, 16.0, 32.0]
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+        "sigma": [1.64, 1.31, 1.0, 0.77, 0.64, 0.73, 0.86, 1.18, 1.5],
+        "epsilon": 0.01,
+        "precision": 2
+    },
+    "evaluation": {
+        "measures": {
+            "t2w": ["sdev", "gini", "entropy", "grad"],
+            "tissues": ["entropy", "label-consistency", "grad(2)"],
+            "structures": ["entropy", "label-consistency"]
+        },
+        "rois": {
+            "structure={l:02d}": ["structures", "all"],
+            "tissue={l:d}": ["tissues", "all"]
+        }
+    },
+    "environment": {
+        "queue": {
+            "short": "local",
+            "long": "local"
+        },
+        "threads": 8
+    }
+}

+ 276 - 0
config/sessions.csv

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+1	255	0	0	1	1	Hippocampus left
+2	0	255	0	1	1	Hippocampus right
+3	255	255	0	1	1	Amygdala left
+4	0	0	255	1	1	Amygdala right
+5	255	255	255	1	1	Anterior temporal lobe, medial part left GM
+6	255	255	255	1	1	Anterior temporal lobe, medial part right GM
+7	255	0	0	1	1	Anterior temporal lobe, lateral part left GM
+8	255	255	255	1	1	Anterior temporal lobe, lateral part right GM
+9	7	255	7	1	1	Gyri parahippocampalis et ambiens anterior part left GM
+10	255	255	7	1	1	Gyri parahippocampalis et ambiens anterior part right GM
+11	7	7	255	1	1	Superior temporal gyrus, middle part left GM
+12	255	7	255	1	1	Superior temporal gyrus, middle part right GM
+13	7	255	255	1	1	Medial and inferior temporal gyri anterior part left GM
+14	248	248	248	1	1	Medial and inferior temporal gyri anterior part right GM
+15	255	14	14	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis anterior part left GM
+16	14	255	14	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis anterior part right GM
+17	255	255	14	1	1	Cerebellum left
+18	14	14	255	1	1	Cerebellum right
+19	255	14	255	1	1	Brainstem, spans the midline
+20	14	255	255	1	1	Insula right GM
+21	241	241	241	1	1	Insula left GM
+22	255	21	21	1	1	Occipital lobe right GM
+23	21	255	21	1	1	Occipital lobe left GM
+24	255	255	21	1	1	Gyri parahippocampalis et ambiens posterior part right GM
+25	21	21	255	1	1	Gyri parahippocampalis et ambiens posterior part left GM
+26	255	21	255	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis posterior part right GM
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+29	255	28	28	1	1	Medial and inferior temporal gyri posterior part left GM
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+34	28	255	255	1	1	Cingulate gyrus, posterior part right GM
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+39	35	35	255	1	1	Parietal lobe left GM
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+45	255	255	42	1	1	Subthalamic nucleus left 
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+48	42	255	255	1	1	Corpus Callosum
+49	150	50	150	1	1	Lateral Ventricle left
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+51	255	255	255	1	1	Anterior temporal lobe, medial part left WM
+52	255	255	255	1	1	Anterior temporal lobe, medial part right WM
+53	255	0	0	1	1	Anterior temporal lobe, lateral part left WM
+54	255	255	255	1	1	Anterior temporal lobe, lateral part right WM
+55	7	255	7	1	1	Gyri parahippocampalis et ambiens anterior part left WM
+56	255	255	7	1	1	Gyri parahippocampalis et ambiens anterior part right WM
+57	7	7	255	1	1	Superior temporal gyrus, middle part left WM
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+61	255	14	14	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis anterior part left WM
+62	14	255	14	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis anterior part right WM
+63	14	255	255	1	1	Insula right WM
+64	241	241	241	1	1	Insula left WM
+65	255	21	21	1	1	Occipital lobe right WM
+66	21	255	21	1	1	Occipital lobe left WM
+67	255	255	21	1	1	Gyri parahippocampalis et ambiens posterior part right WM
+68	21	21	255	1	1	Gyri parahippocampalis et ambiens posterior part left WM
+69	255	21	255	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis posterior part right WM
+70	21	255	255	1	1	Lateral occipitotemporal gyrus, gyrus fusiformis posterior part left WM
+71	234	234	234	1	1	Medial and inferior temporal gyri posterior part right WM
+72	255	28	28	1	1	Medial and inferior temporal gyri posterior part left WM
+73	28	255	28	1	1	Superior temporal gyrus, posterior part right WM
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+78	227	227	227	1	1	Cingulate gyrus, posterior part left WM
+79	255	35	35	1	1	Frontal lobe right WM
+80	35	255	35	1	1	Frontal lobe left WM
+81	255	255	35	1	1	Parietal lobe right WM
+82	35	35	255	1	1	Parietal lobe left WM
+83	146	121	255	1	1	CSF
+84	255	0	0	1	0	Extra-cranial background
+85	255	0	0	1	0	Intra-cranial background
+86	220	220	220	1	1	Thalamus right, low intensity part in T2
+87	255	42	42	1	1	Thalamus left, low intensity part in T2

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