Mirror OSF project y2dq4 (MRtrix tutorial data)
Browse files- .gitattributes +9 -0
- README.md +36 -0
- dti/ad.mif +0 -0
- dti/fa.mif +0 -0
- dti/md.mif +0 -0
- dti/rd.mif +0 -0
- fod/5tt_coreg.mif +3 -0
- fod/5tt_nocoreg.mif +3 -0
- fod/csffod_norm.mif +0 -0
- fod/gmfod_norm.mif +0 -0
- fod/gmwmSeed_coreg.mif +3 -0
- fod/peaks.mif +3 -0
- fod/sub-02_den_preproc_unbiased.mif +3 -0
- fod/wmfod_norm.mif +3 -0
- manifest.json +102 -0
- preprocessed/mask.mif +222 -0
- preprocessed/sub-02_AP.bval +1 -0
- preprocessed/sub-02_AP.bvec +3 -0
- preprocessed/sub-02_den.mif +3 -0
- preprocessed/sub-02_den_preproc.mif +3 -0
- preprocessed/sub-02_den_preproc_unbiased.mif +3 -0
.gitattributes
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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fod/5tt_coreg.mif filter=lfs diff=lfs merge=lfs -text
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fod/5tt_nocoreg.mif filter=lfs diff=lfs merge=lfs -text
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fod/gmwmSeed_coreg.mif filter=lfs diff=lfs merge=lfs -text
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fod/peaks.mif filter=lfs diff=lfs merge=lfs -text
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fod/sub-02_den_preproc_unbiased.mif filter=lfs diff=lfs merge=lfs -text
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fod/wmfod_norm.mif filter=lfs diff=lfs merge=lfs -text
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preprocessed/sub-02_den.mif filter=lfs diff=lfs merge=lfs -text
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preprocessed/sub-02_den_preproc.mif filter=lfs diff=lfs merge=lfs -text
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preprocessed/sub-02_den_preproc_unbiased.mif filter=lfs diff=lfs merge=lfs -text
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README.md
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---
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license: mit
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pretty_name: MRtrix diffusion MRI tutorial data (NeurodeskEDU)
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tags:
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- neuroimaging
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- diffusion-mri
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- mrtrix3
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- education
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size_categories:
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- n<1K
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---
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# MRtrix diffusion MRI tutorial data
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Intermediate results used by the three-part [NeurodeskEDU](https://neurodesk.org/edu/) MRtrix series
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(`examples/diffusion_imaging/MRtrix_1.ipynb` to `MRtrix_3.ipynb`), so that each part can start
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without re-running the previous one.
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This is a mirror of the OSF project [y2dq4](https://osf.io/y2dq4/). It was copied on 2026-10-07 because
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OSF rate-limits (HTTP 429) the downloads made by the notebooks' automated test runs.
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| Folder | Contents | Downloaded by |
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| --- | --- | --- |
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| `preprocessed/` | Part 1 outputs (denoised, preprocessed, bias-corrected DWI; mask; T1w; gradients) | Part 2 |
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| `fod/` | Part 2 outputs (response-function FODs, 5TT image), plus some Part 3 outputs | Part 3 |
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| `dti/`, `tractography/` | Further reference outputs (DTI metrics, track-density image) | none |
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`manifest.json` lists each file's size and SHA-256 hash. The hashes match the ones OSF reports for the
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original files.
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## Source and citation
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- Original data: Hannelore Aerts and Daniele Marinazzo (2018). BTC_preop.
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[OpenNeuro ds001226](https://openneuro.org/datasets/ds001226/versions/00001) (CC0).
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- Processed data: Dörig, M. (2024, November 19). Diffusion MRI Analysis with MRtrix: An Interactive
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Three-Part Series on Neurodesk. [OSF](https://osf.io/y2dq4/). MIT License, © Neurodesk Organisation.
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fod/5tt_coreg.mif
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fod/peaks.mif
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fod/sub-02_den_preproc_unbiased.mif
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fod/wmfod_norm.mif
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manifest.json
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preprocessed/mask.mif
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|
| 1 |
+
mrtrix image
|
| 2 |
+
dim: 96,96,60
|
| 3 |
+
vox: 2.5,2.5,2.5
|
| 4 |
+
layout: -0,+1,+2
|
| 5 |
+
datatype: Bit
|
| 6 |
+
transform: 0.998775317451294, -0.0139464212744386, 0.047469596989542, -111.020295121245
|
| 7 |
+
transform: 0.0208211934027938, 0.98883265243796, -0.147568505994766, -85.8811601421479
|
| 8 |
+
transform: -0.0448814344172466, 0.148376153091205, 0.987912027156327, -56.7593299802008
|
| 9 |
+
command_history: /opt/mrtrix3-3.0.4/bin/mrconvert sub-CON02_ses-preop_acq-AP_dwi.nii.gz sub-02_dwi.mif -fslgrad sub-CON02_ses-preop_acq-AP_dwi.bvec sub-CON02_ses-preop_acq-AP_dwi.bval (version=3.0.4)
|
| 10 |
+
command_history: /opt/mrtrix3-3.0.4/bin/dwidenoise sub-02_dwi.mif sub-02_den.mif -noise noise.mif (version=3.0.4)
|
| 11 |
+
command_history: /opt/mrtrix3-3.0.4/bin/dwifslpreproc sub-02_den.mif sub-02_den_preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options ' --slm=linear --data_is_shelled' (version=3.0.4)
|
| 12 |
+
command_history: /opt/mrtrix3-3.0.4/bin/dwibiascorrect ants sub-02_den_preproc.mif sub-02_den_preproc_unbiased.mif -bias bias.mif (version=3.0.4)
|
| 13 |
+
command_history: /opt/mrtrix3-3.0.4/bin/dwi2mask sub-02_den_preproc_unbiased.mif mask.mif (version=3.0.4)
|
| 14 |
+
comments: TE=1.1e+02;Time=125448.950;phase=1;dwell=0.380
|
| 15 |
+
mrtrix_version: 3.0.4
|
| 16 |
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prior_dw_scheme: 0,0,0,0
|
| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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| 26 |
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| 27 |
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| 28 |
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| 29 |
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|
| 30 |
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| 31 |
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| 32 |
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| 33 |
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+
prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 180 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 181 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 182 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 183 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 184 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 185 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 186 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 187 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 188 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 189 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 190 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 191 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 192 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 193 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 194 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 195 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 196 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 197 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 198 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 199 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 200 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 201 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 202 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 203 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 204 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 205 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 206 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 207 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 208 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 209 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 210 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 211 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 212 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 213 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 214 |
+
prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 215 |
+
prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 216 |
+
prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 217 |
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prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 218 |
+
prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 219 |
+
prior_pe_scheme: 0.0,-1.0,0.0,0.1
|
| 220 |
+
file: . 10832
|
| 221 |
+
END
|
| 222 |
+
|