config json file

How to edit config.json

The config.json file controls everything the container will do.

Fields

• acqd: acquisition phase encoding direction; default: AP
• denoise: perform a principal component analysis (PCA) based denoising of the data (Veraart et al. 2016; Veraart, Fieremans, and Novikov 2016); default: true
• degibbs: perform Gibbs ringing correction (Kellner et al. 2016); default:true
• eddy: perform FSL's eddy current correction; if inverted phase encoding direction files are found, eddy will be done as part of FSL's topup (Andersson and Sotiropoulos 2016); default: true
• eddy_data_is_shelled: do shell checks on diffusion data; default: true
• eddy_slm/eddy_niter/eddy_repol/eddy_mpoder/eddy_slspec: parameters pass to eddy; default: linear/5/true/0/""/
• bias: compute bias correction; default: true
• bias_method: bias correction method to apply if bias field is true; possible methods: ANTs (Tustison et al. 2010) and FSL (Smith, S. M et al. 2004); default: ants
• antsb/antss/antsc: parameters of initial mesh resolution/convergenceThreshold/shrink-factor for ANTs, when dwibiascorrect ants is called; default: [150,3]/[200x200,1e-6]/2
• topup_lambda: replace lambda value in topup; default: "0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001"
• ricn: perform Rician background noise removal; default: true
• norm: perform intensity normalization; default: false
• nval: normalize the intensity of the FA white matter mask to this number; default: 1000
• anatalign: align dwi data with AC-PC anatomy; default: true
• doreslice: do reslicing to the amount set in reslice; default: false
• reslice: if doreslice, reslice the DWI data to an isotropic voxel of this value; default: 1
• saveoutput: save all intermediate files for quality check or debugging; default: true