Commit 11bfdb1a authored by Ludovica Griffanti's avatar Ludovica Griffanti
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# C-MORE brain MRI analysis pipeline
Code for the analysis pipeline presented in the paper "Adapting the UK Biobank brain MRI imaging protocol and analysis pipeline for the C-MORE multi-organ study of COVID-19 survivors"
Used in the project:
> "Capturing MultiORgan Effects of COVID-19’ (C-MORE) study". Details of the main multiorgan study are described [here]
## How to cite
Our preprint is available here
## Contents
* **T1-weighted scan**
This sequence was exactly matched to the one used in UKB and images were processed using the [UKB pipeline](https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1)
* **FLAIR scan**
This sequence was closely matched to the one used in UKB.
Images were processed using the [UKB pipeline](https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1) to extract white matter hyperintensities (WMH).
Additional IDPs extracted in this study:
* Size and FLAIR intensity of the olfactory bulb (OB) - see `OB_pipeline` for details
* Periventricular WMH (PWMH) and deep WMH (DWMH) volumes using the `periventricular_deep_WMH` script
* **Diffusion weighted MRI (dMRI) scan**
In this multiorgan protocol only 3 orthogonal diffusion directions were acquired. The [UKB pipeline](https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1) was used for preprocessing, to derive mean diiffusivity (MD). Average MD was then calculated within an average skeleton in standard space for each tract of the JHU atlas using the `tbss_md` script.
* **Susceptibility-weighted MR Imaging (SWI) scan**
This sequence was closely matched to the one used in UKB.
Images were processed using the [UKB pipeline](https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1) to extract T2* ini 14 structures.
Additional IDPs extracted in this study are quantitative susceptibility mapping (QSM), referenced to CSF, from 14 structures. See `QSM_pipeline` for details
* **Arterial Spin Labelling (ASL)**
This sequence was not included in UKB so far. See `ASL_pipeline` for details on preprocessing pipeline and IDP extraction.
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