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Below are example Snakemake commands, which can be run from the command line, to process dicoms to preprocessed data and scalar maps. These instructions have also been included in the README of the code directory. The Snakemake rules used are listed directly below each command. The filepaths and filenames, which the user must change, are in italics, and any number of files can be converted at once. Importantly, most of the code assumes that the dicom or NIFTI filename matches the name of the folder that it is in. All brain masks (for each MRI contrast) have been provided in the repository and the user should copy the masks to their respective folders, as the code assumes that these masks exist. Alternatively, the user can edit the code to run without masks. Anatomical dataMitra, P. P. Multiple wave-vector extensions of the NMR pulsed-field-gradient spin-echo diffusion measurement. Am. Phys. Soc. 51, 74–78 (1995). Gass, A. et al. Correlation of magnetization transfer ration with clinical disability in multiple sclerosis. Ann. Neurol. 36, 62–67 (1994). Car phone mounts ensure you can enjoy a safe and hands-free driving experience. With suction and vent magnetic phone mounts, we have the ideal accessories to make your commute and trips a doddle. Plus, our smartphone holders are perfect for the home too! 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 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).

All animal procedures were approved by the University of Western Ontario Animal Care Committee and were consistent with guidelines established by the Canadian Council on Animal Care. Twelve adult C57Bl/6 mice (six male and six female) were scanned at six timepoints. They were between 12–14 weeks old at the first timepoint (Fig. 1). Before scanning, anesthesia was induced by placing the animals in an induction chamber with 4% isoflurane and an oxygen flow rate of 1.5 L/min. Following induction, isoflurane was maintained during the imaging session at 1.8% with an oxygen flow rate of 1.5 L/min through a custom-built nose cone. At the end of the study, the mice were euthanized. The mice were anesthetized with ketamine/xylazine (2:1) and then underwent trans-cardiac perfusion with ice-cold saline, followed by 4% paraformaldehyde in phosphate-buffer saline (PBS). In vivo MRI Acquisition mouseID_sex/ timepoint/MTon_GRE_3D_150 × 400_12A_5uT_385FA_3500Hz/MTon_GRE_3D_150 × 400_12A_5uT_385FA_3500Hz_mtsat (in 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). Hammelrath, L. et al. Morphological maturation of the mouse brain: An in vivo MRI and histology investigation. Neuroimage 125, 144–152 (2016). snakemake --cores 1 DiffusionDataPreproc /{ mouse#1_sex /timepoint, mouse#2_sex /timepoint, mouse#3_sex /timepoint}/ dMRI_filename/ dMRI_filename_aveComb_preproc.nii.gzb0 scan acquired with reverse PE (complex-valued data): mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10_b0_reversePE/ uFA_2Shapes_1A_3Rep_TR10_b0_reversePE (in vivo) mouseID_sex/ timepoint/OGSE_5Shapes_1A_5Rep_TR10/OGSE_5Shapes_1A_5Rep_TR10_aveComb_preproc (in vivo) mouseID_sex/ timepoint/ MTon_GRE_3D_100 × 400_36A_5uT_385FA_3500Hz/ MTon_GRE_3D_100 × 400_36A_5uT_385FA_3500Hz_mtr (ex vivo) 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).

mouseID_sex/ timepoint/MTon_GRE_3D_150 × 400_12A_5uT_385FA_3500Hz/MTon_GRE_3D_150 × 400_12A_5uT_385FA_3500Hz_mask (in vivo) Szczepankiewicz, F. et al. Quantification of microscopic diffusion anisotropy disentangles effects of orientation dispersion from microstructure: Applications in healthy volunteers and in brain tumors. Neuroimage 104, 241–252 (2015). 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 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). snakemake --cores 1 Data/{NR1_F/Day0,NR1_F/Day3,NR2_F/Day0}/T2_TurboRARE_AX150150500_A16/T2_TurboRARE_AX150150500_A16.json

Site Customisation

where ‘contrast’ is ‘T2,’ ‘b2000_FA,’ or ‘MTon’ and *** are 3 numbers outputted by the ANTs template building command mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10_b0_reversePE/ uFA_2Shapes_1A_3Rep_TR10_b0_reversePE_aveComb (in vivo) Text file detailing which B1 map slices have artifacts (0 for slices with the banding artifact and 1 for slices without artifacts):

Lema, A. et al. A Comparison of Magnetization Transfer Methods to Assess Brain and Cervical Cord Microstructure in Multiple Sclerosis. J. Neuroimaging 27, 221–226 (2017). Radial Diffusivity (RD) – acquired with b1000 LTE volumes: mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10/uFA_2Shapes_1A_3Rep_TR10_aveComb_preproc_RD mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10/uFA_2Shapes_1A_3Rep_TR10_aveComb_preproc_b2000_FAvec mouseID_sex/ timepoint/uFA_2Shapes_1A_3Rep_TR10/uFA_2Shapes_1A_3Rep_TR10_aveComb_preproc_mean_b0 (in vivo) mouseID_sex/ timepoint/ MTon_GRE_3D_100 × 400_36A_5uT_385FA_3500Hz/ MTon_GRE_3D_100 × 400_36A_5uT_385FA_3500Hz (ex vivo)Veraart, J. et al. Denoising of diffusion MRI using random matrix theory. Neuroimage 142, 394–406 (2016). Tournier, J. D. et al. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. Neuroimage 202, 116137 (2019). snakemake --cores 1 filepath/{ mouse#1_sex /timepoint, mouse#2_sex /timepoint, mouse#3_sex /timepoint}/ dMRI_filename/ dMRI_filename_aveComb.nii.gz