Longitudinal processing #588
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I successfully ran this on a case from OASIS (1mm isotropic, 2 time points). Other resolutions and time points still need testing. The script long_fastsurfer.sh is running a full case with all time points sequentially. The steps are:
2 and 3 can be split into seg_only and surf_only. Also the segmentation of the longitudinal time points in 3 can principally be run in parallel with step 2, only the surface module in 3 needs to wait until the base (step 2) is completely done. |
- Add checks for unsupported run_fastsurfer.sh arguments: --t1, --t2, --sid, --seg_only, surf_only -> --t2 is not currently supported, because this would need adapted pre-processing and multiple images - Consistent formatting of Error Messages - Fix incorrect formatting of arrays (@ vs. *) run_fastsurfer.sh - Change help text for longitudinal flags (point to long_fastsurfer.sh). In most cases, these flags should not be used by regular users, who should use long_fastsurfer.sh instead.
Minor updates to the longitudinal stream
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This PR adds scripts for template creation and running both template (base) and long.
Entry script is long_fastsurfer.sh that runs everything sequentially.