niftkRegMNI-T1-B0.py

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This script is for MS registration preprocessing. It calculates the transformation from Atlas to T1, and form T1 to B0 following the guidelines of: Muhlert et al. JMRI 2013. DOI: 10.1002/jmri.23970

Usage: niftkRegMNI-T1-B0.py -t1 <filename> -t2 <filename> -pd <filename> -b0 <filename> ...

Optional Arguments:
 
  -atlas <filename>      : T1 ATLAS filename 
  -atlas_t2 <filename>   : T2 ATLAS filename 
  -atlas_mask <filename> : Mask ATLAS filename 
  -t1 <filename>         : T1 image filename 
  -t2 <filename>         : T2 image filename
  -pd <filename>         : PD image filename [optional, not required if pseudo T1 is specified]
  -b0 <filename>         : B0 image filename
  -pt1 <filename>        : pseudo T1 input filename [optional, not required if T2 and PD are specified PT1=T2-PD]
  -debug                 : debug mode doesn't delete temporary intermediate images
  -space <value>   : where we want to resampling the images [b0,MNI,T1 or All] Default: B0