Adept R2'

R2' and tat2 for Wellcome Leap ADEPT

Data

The numbered scripts create files in ../data. make (see Makefile) will run only needed scripts for updates in raw.

../data
├── raw        # 01_oac_sync.bash (rsync)
├── BIDS       # 02_bids.bash, 02x_2_fill_missing_json.bash
├── r2prime    # 02_organize_nii.bash, 03_r2prime.bash
├── fmriprep   # 03_fmriprep.bash
└── tat2       # 04_tat2.bash

Local

This repository's primary home is rhea:/Volumes/Hera/Datasets/adept/scripts

R2'

R2Prime here does not take advantage of the newer BIDS-capable main pipeline. 02_organize_nii.bash subverts the BIDS input that would be handled by r2prime-bids. Instead 03_r2prime.bash uses the r2prime repo's internal r2prime script on Olafsson's original file structure.

nT2*/tat2

tat2 should be inversely correlated to R2'. To compare, we need minimally processed BOLD. Using task ("guess") only and avoiding multi-echo rest until we can confirm ME tat2 looks like single echo.

template json

Raw is nifti with sometimes missing .json side car. 02x_2_fill_missing_json.bash creates a template json to use when missing. Scan specific keys to remove were idnetified with

diff \
  <(jq . ../data/BIDS/sub-0008/ses-01/func/sub-*_task-guess_run-01_bold.json)\
  <(jq . ../data/BIDS/sub-0015/ses-01/func/sub-*task-guess_run-01_bold.json)