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end of file diff --git a/FOD/StudyTemplate15MO_FOD.mif b/FOD/StudyTemplate15MO_FOD.mif deleted file mode 120000 index 072d419..0000000 --- a/FOD/StudyTemplate15MO_FOD.mif +++ /dev/null @@ -1 +0,0 @@ -../.git/annex/objects/2v/PV/MD5E-s447127324--7b242cade5274fd99004d109ea4ab940.mif/MD5E-s447127324--7b242cade5274fd99004d109ea4ab940.mif \ No newline at end of file diff --git a/FOD/StudyTemplate18MO_FOD.mif b/FOD/StudyTemplate18MO_FOD.mif deleted file mode 120000 index 2774584..0000000 --- a/FOD/StudyTemplate18MO_FOD.mif +++ /dev/null @@ -1 +0,0 @@ -../.git/annex/objects/5Z/F5/MD5E-s447127316--162cff0b44d053bc14de57477608f289.mif/MD5E-s447127316--162cff0b44d053bc14de57477608f289.mif \ No newline at end of file diff --git a/LICENSE b/LICENSE deleted file mode 100644 index cfe676c..0000000 --- a/LICENSE +++ /dev/null @@ -1,403 +0,0 @@ -Attribution-NonCommercial-NoDerivatives 4.0 International - -======================================================================= - -Creative Commons 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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 deleted file mode 100644 index 036a1ff..0000000 --- a/README.md +++ /dev/null @@ -1,54 +0,0 @@ -# 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 deleted file mode 120000 index 3c40b8c..0000000 --- a/T2WI/StudyTemplate01MO_T2.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../.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 deleted file mode 120000 index 574b7a8..0000000 --- a/T2WI/StudyTemplate03MO_T2.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../.git/annex/objects/19/XW/MD5E-s2785623--dcfba420b1a87705c2fcd8fc6e2e6ea7.nii.gz/MD5E-s2785623--dcfba420b1a87705c2fcd8fc6e2e6ea7.nii.gz \ No newline at end of file diff --git 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