SuPReMo  0.1.1
Transition from nifty-reg resp

If you have used the previous implementation of the generalised image registration and motion-modelling framework called Nifty-Reg-Resp then you will need to adapt the command line parameters according to the table below. SuPReMo has extended functionality over reg-resp.

Parameters:

reg_resp runSupremo Pattern Description
-static -refState [fName] Reference state/static image
-dynamic -dynamic [int] [fName] File containing list of dynamic images and the total number of dynamic images
-surr -surr [int] [fName] File containting the surrogate signal and the number of signals used
-dType -dType [int] Dynamic image data type [0] = full res images, [1] = low res images
-defSpace -defSpace [fName] File name of image that defines the space of the deformed iamges
-mcrType -mcrType [int] Motion compensation [0] none, [1] average weighting, [2] SR, restart, [3] SR update
-maxMCRIt -maxMCRIt [int] Number of iterations used for iterative MCR method
-rcm -outRCM [fName] Path to save the respratory correspondence model (RCM) to
-saveDyn -outSimDyn [fName] Path to save the simulated dynamic images to
-saveMCR -outMCR [fName] Path to save the motion-compensated reconstruction images to
-saveInterMCRs -outInterMCR [fName] Path to save the motion-compensated reconstruction images to
-outInterGrad [fName] Path to save the intermediate gradient to (experimental)
-sx -sx [float] Final grid spacing along x axis (in mm if positive, in voxels if negative)
-sy -sy [float] Final grid spacing along y axis (in mm if positive, in voxels if negative)
-sz -sz [float] Final grid spacing along z axis (in mm if positive, in voxels if negative)
-be -be [float] Bending energy constraint weight
-le [float] Linear energy constraint weight (experimental)
-maxSwitchIt -maxSwitchIt [int] Maximum number of switches between fitting and reconstruction
-ln -ln [int] Number of pypramid levels generated
-lp -lp [int] Number of pypramid levels used
-maxFitIt -maxFitIt [int] Number of iterations to fit the motion model