diff --git a/.datalad/.gitattributes b/.datalad/.gitattributes deleted file mode 100644 index 59157cb..0000000 --- a/.datalad/.gitattributes +++ /dev/null @@ -1,3 +0,0 @@ -config annex.largefiles=nothing -metadata/aggregate* annex.largefiles=nothing -metadata/objects/** annex.largefiles=(anything) diff --git a/.datalad/config b/.datalad/config deleted file mode 100644 index 065493f..0000000 --- a/.datalad/config +++ /dev/null @@ -1,2 +0,0 @@ -[datalad "dataset"] - id = cc5b6a6c-6b4d-4394-856e-a4c2f991b1f6 diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index f866fed..0000000 --- a/.gitattributes +++ /dev/null @@ -1,4 +0,0 @@ -* annex.backend=MD5E -**/.git* annex.largefiles=nothing -README.md annex.largefiles=nothing -LICENSE annex.largefiles=nothing diff --git a/088/627/MD5E-s33142576--02b5f38377b5d268384633b3f1154d4e.nii.gz.log b/088/627/MD5E-s33142576--02b5f38377b5d268384633b3f1154d4e.nii.gz.log new file mode 100644 index 0000000..f18a415 --- /dev/null +++ b/088/627/MD5E-s33142576--02b5f38377b5d268384633b3f1154d4e.nii.gz.log @@ -0,0 +1,3 @@ +1668732283.096279414s 1 2813a771-5117-4f2a-911a-6e1f42b4afd9 +1668732288.802138459s 1 ad1a736f-360e-48b4-9006-df4a453c02da +1668732288.80959295s 1 ad1a736f-360e-48b4-9006-df4a453c02da diff --git a/0a0/c7f/MD5E-s2174501--2bd5f254de885bd22ba10822eefbc0ff.nii.gz.log b/0a0/c7f/MD5E-s2174501--2bd5f254de885bd22ba10822eefbc0ff.nii.gz.log new file mode 100644 index 0000000..1cd41a1 --- /dev/null +++ b/0a0/c7f/MD5E-s2174501--2bd5f254de885bd22ba10822eefbc0ff.nii.gz.log @@ -0,0 +1,3 @@ +1668732281.187261507s 1 2813a771-5117-4f2a-911a-6e1f42b4afd9 +1668732289.985030145s 1 ad1a736f-360e-48b4-9006-df4a453c02da +1668732289.991764815s 1 ad1a736f-360e-48b4-9006-df4a453c02da diff --git a/3fb/0d2/MD5E-s16694--cd929566c0e7098c4e59df8e6d4c280e.json.log b/3fb/0d2/MD5E-s16694--cd929566c0e7098c4e59df8e6d4c280e.json.log new file mode 100644 index 0000000..2b29967 --- /dev/null +++ b/3fb/0d2/MD5E-s16694--cd929566c0e7098c4e59df8e6d4c280e.json.log @@ -0,0 +1,3 @@ +1668732283.102328236s 1 2813a771-5117-4f2a-911a-6e1f42b4afd9 +1668732290.034533767s 1 ad1a736f-360e-48b4-9006-df4a453c02da +1668732290.04095521s 1 ad1a736f-360e-48b4-9006-df4a453c02da diff --git a/5db/dd5/MD5E-s33754185--4cf33111c805339addff1e888dc0b89f.nii.gz.log b/5db/dd5/MD5E-s33754185--4cf33111c805339addff1e888dc0b89f.nii.gz.log new file mode 100644 index 0000000..7e59799 --- /dev/null +++ b/5db/dd5/MD5E-s33754185--4cf33111c805339addff1e888dc0b89f.nii.gz.log @@ -0,0 +1,3 @@ +1668732281.096887839s 1 2813a771-5117-4f2a-911a-6e1f42b4afd9 +1668732287.894948627s 1 ad1a736f-360e-48b4-9006-df4a453c02da +1668732287.903192218s 1 ad1a736f-360e-48b4-9006-df4a453c02da diff --git a/LICENSE b/LICENSE deleted file mode 100644 index da6ab6c..0000000 --- a/LICENSE +++ /dev/null @@ -1,396 +0,0 @@ -Attribution 4.0 International - -======================================================================= - -Creative Commons Corporation ("Creative Commons") is not a law firm and -does not provide legal services or legal advice. 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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 de24006..0000000 --- a/README.md +++ /dev/null @@ -1,46 +0,0 @@ -# BMA 2017 Ex Vivo (Brain Space 1) - -Authors: Alexander Woodward1*, Tsutomu Hashikawa1,2, Masahide Maeda1, Takaaki Kaneko3, Keigo Hikishima4, Atsushi Iriki2, Hideyuki Okano3, Yoko Yamaguchi1* - -1. Neuroinformatics Japan Center, RIKEN Brain Science Institute -2. Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute -3. Laboratory for Marmoset Neural Architecture, RIKEN Brain Science Institute -4. Animal Resources Section, Okinawa Institute of Science and Technology Graduate University - -*corresponding authors: Alexander Woodward (alexander.woodward@riken.jp), Yoko Yamaguchi (yokoy@brain.riken.jp) - -## DATASET DESCRIPTION - -The dataset includes NIfTI files of MRI T2 ex-vivo data; reconstructed Nissl stained images of the same brain, registered to the shape of the MRI; brain region segmentation (with separate color lookup table); and gray, mid-cortical and white matter boundary segmentation. In addition, a 3D Slicer scene file is provided that can be used for testing the dataset within the freely downloadable 3D Slicer software (https://www.slicer.org/). The scene file can be dragged directly into 3D Slicer and the atlas can be used immediately. Files can be downloaded individually or as one zip file. -The atlas can be viewed online via the Zooming Atlas Viewer (ZAV) by clicking here. -KEYWORDS : digital atlas, marmoset, Callithrix jacchus, brain, reference atlas, 3D, NIfTI, brain atlas, 3D Slicer - -## CITATION - -Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko : Brain/MINDS 3D Marmoset Reference Brain Atlas 2017 (DataID: 2799) https://doi.org/10.24475/bma.2799 - -## RELATED PUBLICATION(S) - -The technical details of the data and its generation is available in the following article: - -Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko (2017): The Brain/MINDS 3D digital marmoset brain atlas. https://www.nature.com/articles/sdata20189 - -## CONTENT - -| File name | Description | -| ---- | ---- | -| [`bma-1-mri.nii.gz`](bma-1-mri.nii.gz) | MRI T2 ex-vivo volume (NIfTI-1) | -| [`bma-1-nissl.nii.gz`](bma-1-nissl.nii.gz) | Nissl volume registered to MRI (NIfTI-1) | -| [`bma-1-region_seg.nii.gz`](bma-1-region_seg.nii.gz) | Brain region segmentation volume (NIfTI-1) | -| [`bma-1-graywhite_seg.nii.gz`](bma-1-graywhite_seg.nii.gz) | Gray and white matter boundary segmentation volume (NIfTI-1) | -| [`bma-1-mid_seg.nii.gz`](bma-1-mid_seg.nii.gz) | Mid-cortical boundary segmentation volume (NIfTI-1) | -| [`bma-1-clut.ctbl`](bma-1-clut.ctbl) | Color lookup table for bma-1-regionseg.nii (CTBL) | -| [`bma-1-slicerscene.mrml`](bma-1-slicerscene.mrml) | 3D Slicer scene file (MRML) | -| [`bma-1-mri_unprocessed_exvivo_t2wi.nii.gz`](bma-1-mri_unprocessed_exvivo_t2wi.nii.gz) | Unprocessed MRI T2WI ex-vivo volume with skull (NIfTI-1) | - - -## VERSION HISTORY - -* 22-04-2020 - Updated. Unprocessed MRI T2WI ex-vivo volume with skull was added. -* 22-11-2017 - Initial release. - diff --git a/a04/2a6/MD5E-s919411--3751a31982a918d105d5f49a655c2f34.nii.gz.log b/a04/2a6/MD5E-s919411--3751a31982a918d105d5f49a655c2f34.nii.gz.log new file mode 100644 index 0000000..1111552 --- /dev/null +++ b/a04/2a6/MD5E-s919411--3751a31982a918d105d5f49a655c2f34.nii.gz.log @@ -0,0 +1,3 @@ +1668732281.024140162s 1 2813a771-5117-4f2a-911a-6e1f42b4afd9 +1668732286.930166054s 1 ad1a736f-360e-48b4-9006-df4a453c02da +1668732286.936229645s 1 ad1a736f-360e-48b4-9006-df4a453c02da diff --git a/b63/9db/MD5E-s1225675--9837c8c59e01545445c0990fec769b46.nii.gz.log b/b63/9db/MD5E-s1225675--9837c8c59e01545445c0990fec769b46.nii.gz.log new file mode 100644 index 0000000..55eda4d --- /dev/null +++ b/b63/9db/MD5E-s1225675--9837c8c59e01545445c0990fec769b46.nii.gz.log @@ -0,0 +1,3 @@ +1668732281.017340226s 1 2813a771-5117-4f2a-911a-6e1f42b4afd9 +1668732286.856912872s 1 ad1a736f-360e-48b4-9006-df4a453c02da 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