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Preprocessing Scripts
- Sophie Matis
You can find the job scripts and instructions for running the following pipelines at the links below:
DWI pre-processing with FastSurfer T1 processing (requires slightly more set up but will work better in most cases).
GITHUB:
Rather than creating your own directories and files, the scripts and all reference files can be found and cloned from this private github repository: https://github.com/smmatis/FTDPreprocessing
Please request access from Sophie (sophie.matis@sydney.edu.au).
Change log:
Date updated | Scripts updated | Section updated | Details |
|---|---|---|---|
25/01/2022 | Diffusion_Script1GPU | Run Synb0 | Changed save location of b0 in dwiextract to tmp_dir so it doesn’t save over itself when re-grid in the next step. This was creating blank b0 files in the INPUTS directory for some scans. |
01/02/2022 | Diffusion_Script1_GPU | Notes | Note added to the bottom of the script providing an alternative masking step in case dwi2mask doesn’t do a good job (FSL’s BET tool). |
15/02/2023 | All scripts with XNAT download |
| xnatutils needs to be installed in a python environment now rather than being loaded as a module. Instructions to create the python environment in the users home directory have been added and module load replaced with activating the environment. |
17/02/2023 | Diffusion_Script1_GPU | Eddy | Replaced dwifslpreproc (for eddy and topup) with fsl eddy using the topup outputs from Synb0. The Synb0 topup seems to work much better for our scans. (I have left the old steps commented out incase someone wants to use, just uncomment dwifslpreproc and comment out eddy). |
19/01/2024 | Diffusion_Script1_GPU & Diffusion_Script3CPU | Eddy | Moved eddy from script 1 to script 3 as it runs faster with multiple cores on CPU. |
06/02/2024 | Diffusion_Script3CPU | before FOD generation | Resampling the preprocessed DWI to 1mm instead of 1.25 as it requires less downsampling from the interpolated (0.9375) scans and matches the resolution of the T1. |