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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..036a1ff --- /dev/null +++ b/README.md @@ -0,0 +1,54 @@ +# Brain/MINDS Marmoset MRI age-specific averaged images + +Authors: Akiko Uematsu1, Junichi Hata2, Yuji Komaki3, Fumiko Seki1, Chihoko Yamada3, Norio Okahara3, Yoko Kurotaki3, Erika Sasaki1,2,3, Hideyuki Okano1,2,3* + +1. Department of Physiology (Okano Lab), Keio University School of Medicine, Keio University School of Medicine +2. Laboratory for Marmoset Neural Architecture, RIKEN Brain Science Institute +3. Central Institute for Experimental Animals + +*corresponding author: Hideyuki Okano (hidokano@a2.keio.jp) + +## DATASET DESCRIPTION + +The dataset includes gziped NIfTI files (.nii.gz) of MRI T2WI and DTI metrics (FA, MD, RD, and AD) in-vivo data; the ages of the data are 1,3,6,9,12,15,18 months old. + +The creation process of these averaged images is referred to the script of FSL software (https://fsl.fmrib.ox.ac.uk/), `fslvm_2_template`, partially modified; the non-linear registration process was replaced to the script of ANTs (http://stnava.github.io/ANTs/), `antsRegsitrationSyN.sh`. The details are described in the text “Dataset Description and Image Processing”. + +In addition, age-specific DWI templates (.mif files) are provided, which are created using the script of Mrtrix3 (http://www.mrtrix.org/), `population_template`. +
+You may convert .mif file to NIFTI, extracting b-vector and b-value information by conducting the following Mrtrix3’s command: +``` +# mrconvert dwi_input.mif dwi_output.nii -export_grad_fsl bvec bval +``` + +## CITATION + +Uematsu, Akiko; Hata, Junichi; Komaki, Yuji; Seki, Fumiko; Yamada, Chihoko; Okahara, Norio; Kurotaki, Yoko; Sasaki, Erika; Okano, Hideyuki. +_Brain/MINDS Age-Specific Marmoset Averaged Image Dataset (DataID: 3236)_ +DOI: https://doi.org/10.24475/bminds.mri.kau.3236 + + +## RELATED PUBLICATION(S) + +Uematsu, A., Hata, J., Komaki, Y., Seki, F., Yamada, C., Okahara, N., Okahara., Kurotaki, Y., Sasaki E. & Okano, H. (2017). +_Mapping orbitofrontal-limbic maturation in non-human primates: A longitudinal magnetic resonance imaging study_. NeuroImage 163, 55-67. +DOI: https://doi.org/10.1016/j.neuroimage.2017.09.028 + +## LICENSE + +This work is licensed under a [Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License](http://creativecommons.org/licenses/by-nc-nd/4.0/). + +## CONTENT + +| File name | Description | +| ---- | ---- | +|[`About_ImageProcessing.docx`](About_ImageProcessing.docx)|The details of Dataset Description and Image Processing (.docx)| +|[`T2WI/`](T2WI/)|T2 weighted image at 1,3,6,9,12,15,18 months old. (.nii.gz)| +|[`DTI/`](DTI/)|| +| [`FA/`](DTI/FA/)|Fractional Anisotropy images at 1,3,6,9,12,15,18 months old. (.nii.gz)| +| [`MD/`](DTI/MD/)|Mean Diffusivity images at 1,3,6,9,12,15,18 months old. (.nii.gz)| +| [`RD/`](DTI/RD/)|Radial Diffusivity images at 1,3,6,9,12,15,18 months old. (.nii.gz)| +| [`AD/`](DTI/AD/)|Axial Diffusivity images at 1,3,6,9,12,15,18 months old. (.nii.gz)| +|[`DWI/`](DWI/)|Study and age-specific template of DWI at 1,3,6,9,12,15,18 months old (30 axis with two b0) | +|[`FOD/`](FOD/)|Fiber Orientation Distribution images determined by constrained spherical deconvolution at 1,3,6,9,12,15,18 months old.| + diff --git a/T2WI/StudyTemplate01MO_T2.nii.gz b/T2WI/StudyTemplate01MO_T2.nii.gz new file mode 120000 index 0000000..3c40b8c --- /dev/null +++ b/T2WI/StudyTemplate01MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/22/VZ/MD5E-s3636239--4ff34033f33138109c7c4a2c25d0182f.nii.gz/MD5E-s3636239--4ff34033f33138109c7c4a2c25d0182f.nii.gz \ No newline at end of file diff --git a/T2WI/StudyTemplate03MO_T2.nii.gz b/T2WI/StudyTemplate03MO_T2.nii.gz new file mode 120000 index 0000000..574b7a8 --- /dev/null +++ b/T2WI/StudyTemplate03MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/19/XW/MD5E-s2785623--dcfba420b1a87705c2fcd8fc6e2e6ea7.nii.gz/MD5E-s2785623--dcfba420b1a87705c2fcd8fc6e2e6ea7.nii.gz \ No newline at end of file diff --git a/T2WI/StudyTemplate06MO_T2.nii.gz b/T2WI/StudyTemplate06MO_T2.nii.gz new file mode 120000 index 0000000..0d37fb7 --- /dev/null +++ b/T2WI/StudyTemplate06MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/32/J9/MD5E-s3025257--057720f8b42ce8191a954076d4517fe2.nii.gz/MD5E-s3025257--057720f8b42ce8191a954076d4517fe2.nii.gz \ No newline at end of file diff --git a/T2WI/StudyTemplate09MO_T2.nii.gz b/T2WI/StudyTemplate09MO_T2.nii.gz new file mode 120000 index 0000000..5a03173 --- /dev/null +++ b/T2WI/StudyTemplate09MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/V2/kJ/MD5E-s2943959--079fe1798436921a43b732d7b9912d72.nii.gz/MD5E-s2943959--079fe1798436921a43b732d7b9912d72.nii.gz \ No newline at end of file diff --git a/T2WI/StudyTemplate12MO_T2.nii.gz b/T2WI/StudyTemplate12MO_T2.nii.gz new file mode 120000 index 0000000..70161a5 --- /dev/null +++ b/T2WI/StudyTemplate12MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/Q1/MX/MD5E-s3077004--76a6cc9907afaf754a874475165c26aa.nii.gz/MD5E-s3077004--76a6cc9907afaf754a874475165c26aa.nii.gz \ No newline at end of file diff --git a/T2WI/StudyTemplate15MO_T2.nii.gz b/T2WI/StudyTemplate15MO_T2.nii.gz new file mode 120000 index 0000000..95f15ac --- /dev/null +++ b/T2WI/StudyTemplate15MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/Ww/02/MD5E-s2958812--300d4e97c03cc5ffd8ae6dca23cc6db8.nii.gz/MD5E-s2958812--300d4e97c03cc5ffd8ae6dca23cc6db8.nii.gz \ No newline at end of file diff --git a/T2WI/StudyTemplate18MO_T2.nii.gz b/T2WI/StudyTemplate18MO_T2.nii.gz new file mode 120000 index 0000000..fed2909 --- /dev/null +++ b/T2WI/StudyTemplate18MO_T2.nii.gz @@ -0,0 +1 @@ +../.git/annex/objects/gm/8W/MD5E-s2698255--26bb0f5d16e371ef0d52692f823beef0.nii.gz/MD5E-s2698255--26bb0f5d16e371ef0d52692f823beef0.nii.gz \ No newline at end of file