Folder containing all implemented or developed quantitative spinal cord imaging pipelines and data analyses
Labounek R, Valošek J, Horák T, Svátková A, Bednařík P, Vojtíšek L, Horáková M, Nestrašil I, Lenglet C, Cohen-Adad J, Bednařík J and Hluštík P. HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy. Scientific Reports, 10, 17529. https://doi.org/10.1038/s41598-020-70297-3
Manual draft is available here: https://docs.google.com/document/d/1aH6JeInpfyZSBGaTrPBRDYx8dcrZ15qoXl1m46oKD1s/edit?usp=sharing
Acquired raw data are available here: https://hdl.handle.net/20.500.12618/0000-5c13d342-4798-41d9-8d2a-bf750ab79fdb
If you keep the data folder structure as it is, all bash or matlab scripts should work properly.
If you will find some issue in code or data processing at your site, please report a bug in "Issues" section or do not hestiate to contact us at following email addresses: rlaboune@umn.edu, jan.valosek@fnol.cz
Spinal Cord Toolbox v3.2.3 - git clone --branch v3.2.3 https://github.com/neuropoly/spinalcordtoolbox.git
FSL v5.0.10 - https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
ANTS v2.1.0 - http://stnava.github.io/ANTs/
MATLAB - https://www.mathworks.com/products/matlab.html
NIfTI_tools - https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
HTCondor - https://research.cs.wisc.edu/htcondor/
Copyright 2016-2020 Rene Labounek (1,2,3,4), Jan Valosek (1,2) and Petr Hlustik (1,2)
1 - University Hospital Olomouc, Olomouc, Czech Republic
2 - Palacky University Olomouc, Olomouc, Czech Republic
3 - University Hospital Brno, Brno, Czech Republic
4 - University of Minnesota, Minneapolis, US
sc-dmri-myelopathy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
sc-dmri-myelopathy is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with sc-dmri-myelopathy. If not, see https://www.gnu.org/licenses/.