diff --git a/.datalad/.gitattributes b/.datalad/.gitattributes new file mode 100644 index 0000000..59157cb --- /dev/null +++ b/.datalad/.gitattributes @@ -0,0 +1,3 @@ +config annex.largefiles=nothing +metadata/aggregate* annex.largefiles=nothing +metadata/objects/** annex.largefiles=(anything) diff --git a/.datalad/config b/.datalad/config new file mode 100644 index 0000000..e844b5a --- /dev/null +++ b/.datalad/config @@ -0,0 +1,2 @@ +[datalad "dataset"] + id = 1205a3d4-a592-451a-a049-60687be141e4 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..f866fed --- /dev/null +++ b/.gitattributes @@ -0,0 +1,4 @@ +* annex.backend=MD5E +**/.git* annex.largefiles=nothing +README.md annex.largefiles=nothing +LICENSE annex.largefiles=nothing diff --git a/095/7f8/MD5E-s4121295--757b09c17652b579bf94f00512c5c9b9.surf.gii.log b/095/7f8/MD5E-s4121295--757b09c17652b579bf94f00512c5c9b9.surf.gii.log deleted file mode 100644 index e79e6b0..0000000 --- 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Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. + diff --git a/README.md b/README.md new file mode 100644 index 0000000..2dffc27 --- /dev/null +++ b/README.md @@ -0,0 +1,61 @@ +# BMA 2019 Ex Vivo (Brain Space 2) + +Authors: Alexander Woodward1*, Rui Gong1, Ken Nakae2, Junichi Hata3,4,5, Hideyuki Okano3,4, Shin Ishii2, Yoko Yamaguchi6,7,8 + +1. Connectome Analysis Unit, Integrative Computational Brain Science Collaboration Division, RIKEN Center for Brain Science +2. Integrated Systems Biology Laboratory (Ishii Laboratory), Division of Systems Informatics, Department of Systems Science, Graduate School of Informatics, Kyoto University +3. Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science +4. Department of Physiology (Okano Lab), Keio University School of Medicine, Keio University School of Medicine +5. Division of Regenerative Medicine, Jikei University School of Medicine +6. Applied Electronics Laboratory, Kanazawa Institute of Technology +7. Graduate School of Information Science and Technology, The University Tokyo +8. Laboratory for Cognitive Brain Mapping, RIKEN Center for Brain Science + +*corresponding author: Alexander Woodward (alexander.woodward@riken.jp) + +## DATASET DESCRIPTION + +This atlas is composed of a population average ex-vivo MRI T2WI contrast mapped with the [BMA 2017 Ex Vivo](https://dataportal.brainminds.jp/reference-atlas-data/) (published by Woodward et al. [The Brain/MINDS 3D digital marmoset brain atlas](https://www.nature.com/articles/sdata20189)). +The population average MRI was constructed based on scans of 25 individual brains. The 25 brains were aligned with one another by iteratively applying linear and non-linear registration and averaging the transformation files until convergence. Data of individual brains were then resampled with an isotropic spatial resolution of 100×100×100µm3 and averaged across brain. The registration procedure gave a brain shape with a high signal-to-noise ratio compared to an individual MRI scan. The average MRI was then AC-PC aligned within an RAS (Right-Anterior-Superior) coordinate system. +Cortical flat map and mid-thickness surfaces for the left and right hemispheres are now provided in the common GIFTI format (*. gii) for surface data. These are compatible with [Connectome Workbench](https://www.humanconnectome.org/software/connectome-workbench) (version 1.5.0 and higher) and a Scene file is also provided for easy viewing of the data. +KEYWORDS : digital atlas, marmoset, Callithrix jacchus, brain, reference atlas, 3D, NIfTI, brain atlas, 3D Slicer, flat map, GIfTI, Connectome Workbench + +## CITATION + +Woodward, Alexander; Gong, Rui; Nakae, Ken; Hata, Junichi; Okano, Hideyuki; Ishii, Shin; Yamaguchi, Yoko : Brain/MINDS 3D Marmoset Reference Brain Atlas 2019 (DataID: 4520) https://doi.org/10.24475/bma.4520 + +## LICENSE + +This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). + +## CONTENT + +| File name | Description | +| ---- | ---- | +|[`bma_2019_exvivo`](bma_2019_exvivo)/|Initial package| +|  [`CHANGES.txt`](bma_2019_exvivo/CHANGES.txt)|Change log| +|    [`base_data/`](bma_2019_exvivo/base_data/)|| +|      [`sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz`](bma_2019_exvivo/base_data/sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz)|Population average ex-vivo MRI T2WI N=25| +|    [`labelmap/`](bma_2019_exvivo/labelmap/)|| +|      [`sp2_label_512_3dslicer_v1.0.0.ctbl`](bma_2019_exvivo/labelmap/sp2_label_512_3dslicer_v1.0.0.ctbl)|Color look-up table| +|      [`sp2_label_512_v1.0.0.nii.gz`](bma_2019_exvivo/labelmap/sp2_label_512_v1.0.0.nii.gz)|Atlas region label map| +|    [`transforms/`](bma_2019_exvivo/transforms/)|| +|      [`sp1_to_sp2_affine_v1.0.0.txt`](bma_2019_exvivo/transforms/sp1_to_sp2_affine_v1.0.0.txt)|Linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Affine matrix.| +|      [`sp1_to_sp2_invwarp_v1.0.0.nii.gz`](bma_2019_exvivo/transforms/sp1_to_sp2_invwarp_v1.0.0.nii.gz)|Inverse of non-linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Displacement field.| +|      [`sp1_to_sp2_warp_v1.0.0.nii.gz`](bma_2019_exvivo/transforms/sp1_to_sp2_warp_v1.0.0.nii.gz)|Non-linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Displacement field.| +|[`bma_sp2_cortical_flatmaps`](bma_sp2_cortical_flatmaps)|Flat map package| +|  [`CHANGES.txt`](bma_sp2_cortical_flatmaps/CHANGES.txt)|Change log| +|  [`bma_sp2.lh.cortex.label.gii`](bma_sp2_cortical_flatmaps/bma_sp2.lh.cortex.label.gii)|Left hemisphere cortex region label| +|  [`bma_sp2.lh.flatmap.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.lh.flatmap.surf.gii)|Left hemisphere cortical flat map| +|  [`bma_sp2.lh.graymid.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.lh.graymid.surf.gii)|Left hemisphere cortical mid-thickness surface| +|  [`bma_sp2.rh.cortex.label.gii`](bma_sp2_cortical_flatmaps/bma_sp2.rh.cortex.label.gii)|Right hemisphere cortex region label| +|  [`bma_sp2.rh.flatmap.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.rh.flatmap.surf.gii)|Right hemisphere cortical flat map| +|  [`bma_sp2.rh.graymid.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.rh.graymid.surf.gii)|Right hemisphere cortical mid-thickness surface| +|  [`bma_sp2_connectome_workbench.scene`](bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.scene)|Connectome workbench scene file| +|  [`bma_sp2_connectome_workbench.spec`](bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.spec)|Connectome workbench specification file| + +## VERSION HISTORY + +* 17-06-2021: Added Flat map package. +* 04-02-2020: Initial release. + diff --git a/b30/a2c/MD5E-s2194151--c109c2da046dc4391f1b70db472d81ac.log b/b30/a2c/MD5E-s2194151--c109c2da046dc4391f1b70db472d81ac.log deleted file mode 100644 index 297b8f3..0000000 --- a/b30/a2c/MD5E-s2194151--c109c2da046dc4391f1b70db472d81ac.log +++ /dev/null @@ -1,4 +0,0 @@ -1668732314.725609439s 1 fb52c9c9-ceb4-4c8b-9338-ca758202d24d -1668732335.660973598s 1 03069639-2d89-4297-baa1-4a44648ed722 -1668732335.667656756s 1 03069639-2d89-4297-baa1-4a44648ed722 -1694575010.296041037s 1 b5c72e68-c8c9-42af-883b-8c2834e8452e diff --git a/bb2/665/MD5E-s1085570--16fdb24706f64a387370be759c05dc01.nii.gz.log b/bb2/665/MD5E-s1085570--16fdb24706f64a387370be759c05dc01.nii.gz.log deleted file mode 100644 index e72a1de..0000000 --- a/bb2/665/MD5E-s1085570--16fdb24706f64a387370be759c05dc01.nii.gz.log +++ /dev/null @@ -1,3 +0,0 @@ -1668732311.844012254s 1 fb52c9c9-ceb4-4c8b-9338-ca758202d24d -1668732323.444220149s 1 03069639-2d89-4297-baa1-4a44648ed722 -1668732323.450994736s 1 03069639-2d89-4297-baa1-4a44648ed722 diff --git a/bma_2019_exvivo/CHANGES.txt b/bma_2019_exvivo/CHANGES.txt new file mode 120000 index 0000000..79bc9ab --- /dev/null +++ b/bma_2019_exvivo/CHANGES.txt @@ -0,0 +1 @@ +../.git/annex/objects/9W/mp/MD5E-s42--1ff420d2812eb77d16eeb6ed3ac6c1ce.txt/MD5E-s42--1ff420d2812eb77d16eeb6ed3ac6c1ce.txt \ No newline at end of file diff --git a/bma_2019_exvivo/base_data/sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz b/bma_2019_exvivo/base_data/sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz new file mode 120000 index 0000000..e0ab76e --- /dev/null +++ b/bma_2019_exvivo/base_data/sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz @@ -0,0 +1 @@ +../../.git/annex/objects/52/gF/MD5E-s178237208--d85ea316f45df9f9ada2fab48dd9f8cf.nii.gz/MD5E-s178237208--d85ea316f45df9f9ada2fab48dd9f8cf.nii.gz \ No newline at end of file diff --git a/bma_2019_exvivo/labelmap/sp2_label_512_3dslicer_v1.0.0.ctbl b/bma_2019_exvivo/labelmap/sp2_label_512_3dslicer_v1.0.0.ctbl new file mode 120000 index 0000000..3e00307 --- /dev/null +++ b/bma_2019_exvivo/labelmap/sp2_label_512_3dslicer_v1.0.0.ctbl @@ -0,0 +1 @@ +../../.git/annex/objects/Wz/M5/MD5E-s91704--65743cc1541baaf3b4c500bfc3095066.0.ctbl/MD5E-s91704--65743cc1541baaf3b4c500bfc3095066.0.ctbl \ No newline at end of file diff --git a/bma_2019_exvivo/labelmap/sp2_label_512_v1.0.0.nii.gz b/bma_2019_exvivo/labelmap/sp2_label_512_v1.0.0.nii.gz new file mode 120000 index 0000000..00bc984 --- /dev/null +++ b/bma_2019_exvivo/labelmap/sp2_label_512_v1.0.0.nii.gz @@ -0,0 +1 @@ +../../.git/annex/objects/MV/Kg/MD5E-s1085570--16fdb24706f64a387370be759c05dc01.nii.gz/MD5E-s1085570--16fdb24706f64a387370be759c05dc01.nii.gz \ No newline at end of file diff --git a/bma_2019_exvivo/transforms/sp1_to_sp2_affine_v1.0.0.txt b/bma_2019_exvivo/transforms/sp1_to_sp2_affine_v1.0.0.txt new file mode 120000 index 0000000..f7e67b5 --- /dev/null +++ b/bma_2019_exvivo/transforms/sp1_to_sp2_affine_v1.0.0.txt @@ -0,0 +1 @@ +../../.git/annex/objects/jG/z6/MD5E-s419--4c192150cb681874b9198ae9047bec13.0.txt/MD5E-s419--4c192150cb681874b9198ae9047bec13.0.txt \ No newline at end of file diff --git a/bma_2019_exvivo/transforms/sp1_to_sp2_invwarp_v1.0.0.nii.gz b/bma_2019_exvivo/transforms/sp1_to_sp2_invwarp_v1.0.0.nii.gz new file mode 120000 index 0000000..b790ae8 --- /dev/null +++ b/bma_2019_exvivo/transforms/sp1_to_sp2_invwarp_v1.0.0.nii.gz @@ -0,0 +1 @@ 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No newline at end of file diff --git a/bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.spec b/bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.spec new file mode 120000 index 0000000..3e28593 --- /dev/null +++ b/bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.spec @@ -0,0 +1 @@ +../.git/annex/objects/j9/37/MD5E-s1020--88ce29411cde47e9125ab651e2cf3148.spec/MD5E-s1020--88ce29411cde47e9125ab651e2cf3148.spec \ No newline at end of file diff --git a/c29/226/MD5E-s214965724--a9282d6266f35568088e5b4bce168145.nii.gz.log b/c29/226/MD5E-s214965724--a9282d6266f35568088e5b4bce168145.nii.gz.log deleted file mode 100644 index 062c1ca..0000000 --- a/c29/226/MD5E-s214965724--a9282d6266f35568088e5b4bce168145.nii.gz.log +++ /dev/null @@ -1,3 +0,0 @@ -1668732312.667755274s 1 fb52c9c9-ceb4-4c8b-9338-ca758202d24d -1668732334.807522064s 1 03069639-2d89-4297-baa1-4a44648ed722 -1668732334.815416637s 1 03069639-2d89-4297-baa1-4a44648ed722 diff --git 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