Commit 446e0f7d authored by Ludovica Griffanti's avatar Ludovica Griffanti
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Update README.md

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......@@ -11,18 +11,18 @@ Our preprint is available [here](https://www.medrxiv.org/content/10.1101/2021.05
## Contents
* **T1-weighted.**
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)
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/open-science/analysis/UK_biobank_pipeline_v_1)
* **T2-FLAIR.**
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).
Images were processed using the [UKB pipeline](https://git.fmrib.ox.ac.uk/open-science/analysis/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 `bianca_perivent_deep` script
* **Diffusion weighted MRI (dMRI).**
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 therefore adapted for preprocessing the images and derive mean diffusivity (MD) IDPs. Scripts are in the `dMRI_pipeline` folder. Preprocessing was performed using the `cmore_diff.sh` script. Average MD was then calculated within an average skeleton in standard space for each tract of the JHU atlas using the `cmore_tbss_md` script (modified from bb_tbss of the UKB pipeline) and also within the normal appearing white matter only (i.e. outside WMH) using the `cmore_tbss_md_NAWM` script.
In this multiorgan protocol only 3 orthogonal diffusion directions were acquired. The [UKB pipeline](https://git.fmrib.ox.ac.uk/open-science/analysis/UK_biobank_pipeline_v_1) was therefore adapted for preprocessing the images and derive mean diffusivity (MD) IDPs. Scripts are in the `dMRI_pipeline` folder. Preprocessing was performed using the `cmore_diff.sh` script. Average MD was then calculated within an average skeleton in standard space for each tract of the JHU atlas using the `cmore_tbss_md` script (modified from bb_tbss of the UKB pipeline) and also within the normal appearing white matter only (i.e. outside WMH) using the `cmore_tbss_md_NAWM` script.
* **Susceptibility-weighted MR Imaging (SWI).**
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* in 14 structures.
Images were processed using the [UKB pipeline](https://git.fmrib.ox.ac.uk/open-science/analysis/UK_biobank_pipeline_v_1) to extract T2* in 14 structures.
Additional IDPs extracted in this study are quantitative susceptibility mapping (QSM) values, referenced to the CSF QSM value, from 14 structures. See `QSM_pipeline` for details
* **Arterial Spin Labelling (ASL).**
This sequence was not included in UKB at the time of this study. See `ASL_pipeline` for details on preprocessing pipeline and IDP extraction.
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