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Preprocessing Scripts

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You can find the job scripts and instructions for running the following pipelines at the links below:

  1. /wiki/spaces/FN/pages/2557411524

  2. /wiki/spaces/FN/pages/2558722126 (requires slightly more set up but will work better in most cases).

  3. DWI pre-processing with FastSurfer + Connectomics.

  4. /wiki/spaces/FN/pages/2556985575

** I need to add synb0 ref files set up + edit ref_path into these instructions. **

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).

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