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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 deleted file mode 100644 index 2dffc27..0000000 --- a/README.md +++ /dev/null @@ -1,61 +0,0 @@ -# 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 new file mode 100644 index 0000000..297b8f3 --- /dev/null +++ b/b30/a2c/MD5E-s2194151--c109c2da046dc4391f1b70db472d81ac.log @@ -0,0 +1,4 @@ +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 new file mode 100644 index 0000000..e72a1de --- /dev/null +++ b/bb2/665/MD5E-s1085570--16fdb24706f64a387370be759c05dc01.nii.gz.log @@ -0,0 +1,3 @@ +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 deleted file mode 120000 index 79bc9ab..0000000 --- a/bma_2019_exvivo/CHANGES.txt +++ /dev/null @@ -1 +0,0 @@ -../.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 deleted file mode 120000 index e0ab76e..0000000 --- a/bma_2019_exvivo/base_data/sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../.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 deleted file mode 120000 index 3e00307..0000000 --- a/bma_2019_exvivo/labelmap/sp2_label_512_3dslicer_v1.0.0.ctbl +++ /dev/null @@ -1 +0,0 @@ -../../.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 deleted file mode 120000 index 00bc984..0000000 --- a/bma_2019_exvivo/labelmap/sp2_label_512_v1.0.0.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../.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 deleted file mode 120000 index f7e67b5..0000000 --- a/bma_2019_exvivo/transforms/sp1_to_sp2_affine_v1.0.0.txt +++ /dev/null @@ -1 +0,0 @@ -../../.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 deleted file mode 120000 index b790ae8..0000000 --- a/bma_2019_exvivo/transforms/sp1_to_sp2_invwarp_v1.0.0.nii.gz +++ /dev/null @@ -1 +0,0 @@ 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a/bma_sp2_cortical_flatmaps/bma_sp2.lh.cortex.label.gii b/bma_sp2_cortical_flatmaps/bma_sp2.lh.cortex.label.gii deleted file mode 120000 index ce5fd9b..0000000 --- a/bma_sp2_cortical_flatmaps/bma_sp2.lh.cortex.label.gii +++ /dev/null @@ -1 +0,0 @@ -../.git/annex/objects/GW/jV/MD5E-s60304--ad06c0cb97da13db173d997c20977f1a.gii/MD5E-s60304--ad06c0cb97da13db173d997c20977f1a.gii \ No newline at end of file diff --git a/bma_sp2_cortical_flatmaps/bma_sp2.lh.flatmap.surf.gii b/bma_sp2_cortical_flatmaps/bma_sp2.lh.flatmap.surf.gii deleted file mode 120000 index 49109e5..0000000 --- a/bma_sp2_cortical_flatmaps/bma_sp2.lh.flatmap.surf.gii +++ /dev/null @@ -1 +0,0 @@ -../.git/annex/objects/Vz/wg/MD5E-s3033128--a252f9d0a5f30826b88e4f16d27f568b.surf.gii/MD5E-s3033128--a252f9d0a5f30826b88e4f16d27f568b.surf.gii \ No newline at end of file diff --git a/bma_sp2_cortical_flatmaps/bma_sp2.lh.graymid.surf.gii b/bma_sp2_cortical_flatmaps/bma_sp2.lh.graymid.surf.gii deleted file mode 120000 index 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timestamp=1668732304.396025859s