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history_of_lifefu_preprocessing.md

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History of preprocessing LIFE FOLLOWUP

  • beginning of data acquisition for followup in June 2018 basic environment: MRICRON AFNI --version '17.2.17' ANTSENV --version '2.2.0' FSL --version 5.0.9 FREESURFER --version 5.3.0 nipype versions 0.13.0-geb8a930.dev or 1.1.2

Explanation of this pipeline:

structural
Freesurfer v. 5.3.0 was selected for compatibility with baseline data

DWI
Eddy_openmp wrapped for nipype with an in-house implementation (which used /data/pt_life_dti/scripts/life2018/eddy_openmp-5.0.11 but did not allow all output files).
eddy options: - repol -> to interpolate slices with signal loss due to head motion - slice-to-volume correction -> not implemented because the data is single-banded

rs
Preprocessing steps are according to fMRIprep's minimal preprocessing.

Changes to this pipeline:

  • 17.12.2018: rerun all participants because of wrong acquisition time in DWI preprocessing. Previous: total acquisition time = 0.029925, corrected: total acquisition time = 0.05985

  • 21.05.2019: updated EDDY DWI correction to nipype implementation of FSL 5.0.11 (nipype 1.2.0)
    This should not change the results but just enable saving all outputs, to run eddy_quad quality control (from FSL 6.0.1. At this point all participants assessed until now were rerun with run_workflow_redo_eddy.py to re-generate outputs (which only reruns diffusion pipeline)

  • 15.04.2021: modified workflow to use new IDs for FreeSurfer processing and BIDS conversion included in the workflow.

  • 21.04.2021: modified dimension along which images are selected in reports because of differences in conversion between dcm2nii and dcm2niix