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I think you have two independent problems. For the one that results in an empty corratio_dof.nii.gz, I can't see an easy answer, but it could be related to differing file interpretations. Compare the output of "fslinfo" and IRTK "info" (especially the range, line 20 in info output) for the input images and see if you find anything unexpected. The second problem is more straightforward, I think. In your Paper_parameters.txt, make sure that there is no space character (or other whitespace) following the word "True". IRTK is finicky that way. Hope that helps Rolf On Fri, Oct 02, 2009 at 09:40:49AM +0100, Xi Liang wrote: > 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 -- Rolf A Heckemann, MD PhD Médecin chercheur Fondation Neurodis CERMEP - Imagerie du Vivant Hôpital Neurologique Pierre Wertheimer 59 Boulevard Pinel 69003 Lyon 1254475585