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| # This is a template for a FSL tool section # Create subpages as ToolName/blah # Minimum required subpages are: # UserGuide # Faq # Theory # You should also create a ToolName/Contents which contains nothing but the names of the subpages in the order you wish them to appear in the menu, one per line # eg: #UserGuide #Faq #Theory # Do not include the top level page # Attach an image to this page and change the attachment line at the start to show it on the right of the page. # Remember to add this page to the appropriate category = WARNING This page is being edited in preparation for a new release = |
# This is a template for a FSL tool section # Create subpages as ToolName/blah # Minimum required subpages are: # UserGuide # Faq # Theory # You should also create a ToolName/Contents which contains nothing but the names of the subpages in the order you wish them to appear in the menu, one per line # eg: #UserGuide #Faq #Theory # Do not include the top level page # Attach an image to this page and change the attachment line at the start to show it on the right of the page. # Remember to add this page to the appropriate category |
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| = Introduction = | |
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If you use EDDY QC in your research, please make sure that you reference the article listed below. |
If you use EDDY QC in your research, please make sure that you reference the article listed below: |
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| Bastiani, M., Cottaar, M., Fitzgibbon, S.P., Sotiropoulos, S.N., Jbabdi, S., and Andersson, J. Automated quality control for within and between diffusion MRI studies using a non-parametric framework for movement and distortion correction !NeuroImage (submitted) | Bastiani, M., Cottaar, M., Fitzgibbon, S.P., Suri, S., Alfaro-Almagro, F., Sotiropoulos, S.N., Jbabdi, S., and Andersson, J.L.R. Automated quality control for within and between diffusion MRI studies using a non-parametric framework for movement and distortion correction. !NeuroImage, 184:801-812, 2019. |
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| The main reference that should be cited when using EDDY is: {{{#!wiki references Andersson, J.L.R. and Sotiropoulos, S.N. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. !NeuroImage, 125:1063-1078, 2016. }}} If you use the --repol (replace outliers) option, please also reference: {{{#!wiki references Andersson, J.L.R., Graham, M.S., Zsoldos, E., and Sotiropoulos, S.N. Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images. !NeuroImage, 141:556-572, 2016. }}} If you use the slice-to-volume motion model (accessed by the --mporder option) please also reference: {{{#!wiki references Andersson, J.L.R., Graham, M.S., Drobnjak, I., Zhang, H., Filippini, N., and Bastiani, M. Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement. !NeuroImage, 152:450-466, 2017. }}} |
Contents
- Introduction
Contents
- Users Guide
Diffusion MRI (dMRI) data can be affected by hardware and subject-related artefacts that can significantly bias downstream analyses. Therefore, automated quality control (QC) is of great importance to detect data acquisition and pre-processing issues. This is especially critical in large population studies, where manual QC is not practical. The automated EDDY QC framework allows to assess dMRI data both at the single subject and group levels. The QC metrics are derived through different stages of FSL’s pre-processing tools (TOPUP and EDDY). Using this framework it is possible to distinguish between good and bad quality datasets and, importantly, identify subsets of the data that may need careful visual inspection.
References
If you use EDDY QC in your research, please make sure that you reference the article listed below:
Bastiani, M., Cottaar, M., Fitzgibbon, S.P., Suri, S., Alfaro-Almagro, F., Sotiropoulos, S.N., Jbabdi, S., and Andersson, J.L.R. Automated quality control for within and between diffusion MRI studies using a non-parametric framework for movement and distortion correction. NeuroImage, 184:801-812, 2019.
The main reference that should be cited when using EDDY is:
Andersson, J.L.R. and Sotiropoulos, S.N. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage, 125:1063-1078, 2016.
If you use the --repol (replace outliers) option, please also reference:
Andersson, J.L.R., Graham, M.S., Zsoldos, E., and Sotiropoulos, S.N. Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images. NeuroImage, 141:556-572, 2016.
If you use the slice-to-volume motion model (accessed by the --mporder option) please also reference:
Andersson, J.L.R., Graham, M.S., Drobnjak, I., Zhang, H., Filippini, N., and Bastiani, M. Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement. NeuroImage, 152:450-466, 2017.