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Hi, The general approach is right, but there are a few problems with the implementation. a) you should always use a config file with fnirt (e.g. T1_2_MNI152_2mm.cnf in your case) b) you also need to include the flirt matrix result (T1 to mprage) in the call to fnirt (with the --aff option) c) the applywarp command is wrong - you do not need to include the matrix from the T1 to MNI (as this is contained in the warp output from fnirt) but you must include the matrix from the first step (the b0 to mprage result) as the premat d) you should use 6 DOF in the first step, as it is within-subject All the best, Mark On 5 Dec 2013, at 20:30, Bedda Rosario <[log in to unmask]> wrote: > Hello, > > I am trying to do some voxel based analysis for gray matter mean diffusivity. Therefore. I need to register the mean diffusivity image to the MNI template. I tried the following for one subject, however, results don't look good. > > Here it is what I did > > 1. register the b0 to the mprage using flirt. The b0 and MD images are in the same space > 2. register mprage to MNI using flirt > 3. non linear registration, mprage to MNI using fnirt > 4. apply the parameters from 3 to the MD images > > $FSLDIR/bin/flirt -in 5104_avgboraw.nii -ref 5104_mprage.nii -omat flirtbompragemat_5104.mat -out flirt5104_bomprage > > $FSLDIR/bin/flirt -in 5104_mprage.nii -ref /usr/local/fsl-4.1.4/data/standard/MNI152_T1_1mm.nii.gz -omat flirtmprageMNImat_5104.mat -out flirt5104_mprageMNI > > $FSLDIR/bin/fnirt --ref=/usr/local/fsl-4.1.4/data/standard/MNI152_T1_1mm.nii.gz --in=flirt5104_mprageMNI.nii --iout=fnirt5104_mprageMNI --cout=fnirtcout_5104 --fout=fnirtfout_5104 --jout=fnirtjout_5104 --intout=fnirtintout_5104 --logout=fnirtlogout_5104 > > $FSLDIR/bin/applywarp --ref=/usr/local/fsl-4.1.4/data/standard/MNI152_T1_1mm.nii.gz --in=5104_MD.nii --out=5104_MDinMNI --warp=fnirtcout_5104 --premat=flirtmprageMNImat_5104.mat > > Is this approach correct? Any suggestions? > > Thank you, > Bedda