You can find the job scripts and instructions for running the following pipelines at the links below:
/wiki/spaces/FN/pages/2558722126 (requires slightly more set up but will work better in most cases).
** I need to add synb0 ref files set up + edit ref_path into these instructions. **
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. |
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