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Folder containing all implemented or developed quantitative spinal cord imaging pipelines and data analyses

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sc-dmri-myelopathy

Folder containing all implemented or developed quantitative spinal cord imaging pipelines and data analyses

Please, cite as:

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:

Manual draft is available here: https://docs.google.com/document/d/1aH6JeInpfyZSBGaTrPBRDYx8dcrZ15qoXl1m46oKD1s/edit?usp=sharing

Data:

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.

Contact us:

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

Requirements:

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 statement:

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/.