LongitudinalThickness

Development of longitudinal cortical thickness pipelines.

FTDC-PICSL tools for longitudinal thickness

• T1wPreprocessing conforms data orientation, does GPU-accelerated brain extraction using HD-BET, and outputs a QC image. Optionally, it will also perform neck trimming.

• antsnetct performs neck trimming, brain extraction, segmentation, cortical thickness estimation, and normalization to a template. Both cross-sectional and longitudinal pipelines are supported.

• SynthSeg runs synthseg on the GPU and can generate priors for antsnetct.

All of these have wrapper scripts for PMACS users under

/project/ftdc_pipeline/ftdc-picsl