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Rahman, N., Xu, K., Budde, M., Brown, A. & Baron, C. A longitudinal microstructural MRI dataset in healthy C57Bl/6 mice at 9.4 Tesla. Federated Research Data Repository https://doi.org/10.20383/103.0594 (2022). FAtemplate_to_T2template/FA_T2_SynMI0_005_transform1InverseWarp.nii.gz (inverse symmetric diffeomorphic transform) Note that the code assumes that the original NIFTI files are located in the “Data” folder and that FSL is being run from a singularity container. The user can change the code in “dMRIpreproc.sh” located in the folder “code_scidata_paper/dMRIpreproc” to align with their FSL environment. The above command will work with or without reverse phase-encoded data. Enhance your everyday life and make your device more useful. Whether you have an iPhone, Samsung Galaxy or Google Pixel, we have the accessories you need to get the best from your smartphone. And that is exactly what our phone mounts do! Combine our Limitless case range with our Limitless magnetic mounts to make your smartphone instantly way more useful. Each dMRI protocol was acquired with single-shot spin echo echo-planar-imaging (EPI) readout with partial Fourier imaging in the phase encode direction with 80% of k-space being sampled. For each dMRI protocol, a single reverse phase encoded b = 0 s/mm 2 volume was acquired at the end of the diffusion sequence for subsequent use in TOPUP 29 and EDDY 30, from FMRIB Software Library (FSL, Oxford, UK) 31, to correct for susceptibility and eddy current induced distortions.

Tu, T. W. et al. Abnormal injury response in spontaneous mild ventriculomegaly wistar rat brains: A pathological correlation study of diffusion tensor and magnetization transfer imaging in mild traumatic brain injury. J. Neurotrauma 34, 248–256 (2017). snakemake --cores 1 filepath/{ mouse#1_sex /timepoint, mouse#2_sex /timepoint, mouse#3_sex /timepoint}/ dMRI_filename/ dMRI_filename_aveComb_preproc_mean_b0_Wmask.nii.gz

For ex vivo data, as mouse IDs NR7_M and NR8_M were scanned with the skull removed, slight deformation of the tissue is observed at the superior edges of the brain. Mouse IDs NR1_F and NR2_F show banding artifacts in the caudal region of the brain in the B1 maps. Test-retest reproducibility

Arbabi, A., Kai, J., Khan, A. R. & Baron, C. A. Diffusion dispersion imaging: Mapping oscillating gradient spin-echo frequency dependence in the human brain. Magn. Reson. Med. 83, 2197–2208 (2020). mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10/uFA_2Shapes_1A_3Rep_TR10_aveComb_preproc_uA Microscopic Fractional Anisotropy (µFA):

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mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10/uFA_2Shapes_1A_3Rep_TR10_aveComb_preproc_b1000_FAvec mouseID_sex/ timepoint/ MTon_GRE_3D_100 × 400_36A_5uT_385FA_3500Hz/ MTon_GRE_3D_100 × 400_36A_5uT_385FA_3500Hz_mtsat (ex vivo) Yarnykh, V. L. Actual flip-angle imaging in the pulsed steady state: A method for rapid three-dimensional mapping of the transmitted radiofrequency field. Magn. Reson. Med. 57, 192–200 (2007). Rahman, N., Ramnarine, J., Xu, K., Brown, A. & Baron, C. Test-retest reproducibility of in vivo magnetization transfer ratio and saturation index in mice at 9.4 Tesla. J Magn Reson Imaging 1–11, https://doi.org/10.1002/jmri.28106 (2022). The workflow, called the “Snakefile,” contains all data analysis steps such as DICOM to NIFTI conversion, preprocessing data, and scalar map generation. This involves FSL 31, MRtrix3 38, and ANTs 40 commands, as well as MATLAB functions and bash scripts. Users can easily modify and add rules to the pipeline. Example snakemake usage

After combined averages and initial dMRI brain masks are generated, preprocessing can be run by this command: Veraart, J. et al. Denoising of diffusion MRI using random matrix theory. Neuroimage 142, 394–406 (2016). The MT protocol required 50 minutes total scan time and comprised three FLASH-3D (fast low angle shot) scans and one RF transmit field (B1) map scan acquired using the actual flip-angle imaging (AFI) method 33 to correct for local variations in flip angle. An MT-weighted scan, and reference T1-weighted and PD-weighted scans (MTw, T1w, and PDw respectively) were acquired by appropriate choice of the repetition time (TR) and the flip angle (α). MT-weighting was achieved by applying an off-resonance Gaussian-shaped RF pulse (12 ms duration, 385° nominal flip angle, 3.5 kHz frequency offset from water resonance, 5 µT RF peak amplitude) prior to the excitation. Ex vivo MRI Acquisition snakemake --cores 1 filepath/{ mouse#1_sex /timepoint, mouse#2_sex /timepoint, mouse#3_sex /timepoint}/ dMRI_filename/ dMRI_filename_aveComb_preproc_mask.nii.gz Baron, C. A. & Beaulieu, C. Oscillating gradient spin-echo (OGSE) diffusion tensor imaging of the human brain. Magn. Reson. Med. 72, 726–736 (2014).

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MTtemplate_to_T2template/ MT_T2_SynCI0.005__transform1Warp.nii.gz (symmetric diffeomorphic transform) Hagiwara, A. et al. Myelin Measurement: Comparison between Simultaneous Tissue Relaxometry, Magnetization Transfer Saturation Index, and T1w/T2w Ratio Methods. Sci. Rep. 8, 1–12 (2018). Xu, J. Probing neural tissues at small scales: Recent progress of oscillating gradient spin echo (OGSE) neuroimaging in humans. J. Neurosci. Methods 349, 109024 (2021).

Rahman, N. et al. Test-retest reproducibility of in vivo oscillating gradient and microscopic anisotropy diffusion MRI in mice at 9.4 Tesla. PLoS One 16, e0255711 (2021). mouseID_sex/ timepoint/MTon_GRE_3D_150 × 400_12A_5uT_385FA_3500Hz/ MTon_GRE_3D_150 × 400_12A_5uT_385FA_3500Hz (in vivo) mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10/uFA_2Shapes_1A_3Rep_TR10_aveComb_preproc_mask (in vivo)mouseID_sex/ timepoint/OGSE_5Shapes_1A_5Rep_TR10/OGSE_5Shapes_1A_5Rep_TR10_aveComb_preproc_delMD (in vivo)