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?
