Use Synb0-DISCO for TOPUP and eddy

[tombresser]

Modification: If acqpFile exists and has the required dimensions, it can directly be used in the preprocessing steps. Otherwise acqpFile is created according to the original code.

Problem: Some Topup cases require a specific acqpFile. Tool such as SynB0-DISCO can synthesize a b0 image for diffusion distortion correction. When running Topup, the acqpFile should contain two rows in the same direction (see example below). CATO currently auto generates an acqpFile and overwrites existing files in the location.

$ cat acqparams.txt 
0 1 0 0.062
0 1 0 0.000

[tombresser]

First commit was insufficient to make CATO compatible with synb0-DISCO undistorted b0 images.

Issue: CATO expects reverse encoded scans when preparing+running TOPUP and eddy. Synb0-DISCO is a toolbox to estimate undistorted b0 images based on the distorted b0 and a T1 scan. The distorted+undistorted b0 images can be used to run TOPUP and eddy to correct for distortions. However, the undistorted image is not a reverse encoded scan. Hence it is important to provide an acqp.txt with the correct directions and totalreadout times.

Modifications:

• synb0File prameter added to configFile
• preprocess_topup_eddy_synb0.sh added
  • uses synb0Fila to run TOPUP
  • runs eddy on the original dwi file (does not contain the undistorted b0)
  • Added "Case 4: SynB0-DISCO output is available.." to structural_preprocessing.m
  • reads acqpFile and indexFile when synb0File is present
  • basic checks + error messages
  • store copy of acqp and index in CATO output dir
  • checks if dwiFile and synb0File have even dimensions (required for TOPUP)
  • added synb0File to structuralParameterProperties.xlsx