I am using IRTK to register two breast MRI image with contrast. I first use
FLIRT to linear register two images, and then use IRTK to do the norigid part. I
met two problems. The first one is I cannot transform the target image to the
source image by .dof, which is converted from .mat (FSL). The second issue is
nreg( in IRTK) terminates somehow. Could you see something i did wrong?
The follwoings are the scripts I used.
# linear register the images by FLIRT and get output.mat
flirt -in target.nii.gz -ref source.nii.gz -out output.nii.gz -omat output.mat
# convert output.mat to output.dof
flirt2dof corratio.mat target.nii.gz source.nii.gz corratio.dof
# transform target image (all intensity in corratio_dof.nii.gz is 0)
transformation target.nii.gz corratio_dof.nii.gz -dofin corratio.dof
# Because the corratio.dof seems doesnt work, I use output.nii.gz to register
to source.nii.gz directly. The parameters are download from Arno Klein's mindlog
website.
nreg corratio.nii.gz source.nii.gz -parin Paper_parameters.txt -dofout
nonrigid.dof
## Then the following information is given, and the nreg program is terminated
and no nonrigid.dof is produced.
Reading target ... done
Reading source ... done
Lambda 1 is ... 0
Lambda 2 is ... 0
Lambda 3 is ... 0
Control point spacing in X is ... 20
Control point spacing in Y is ... 20
Control point spacing in Z is ... 20
Can't read boolean value = True
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