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Dear FSL experts, i am reposting this query, can someone please help me in this ? Thanks and best Rabia On Sat, Jan 21, 2017 at 6:22 PM, Rabia Mazhar <[log in to unmask]> wrote: > Dear FSL experts, > Is there a command line way to do non linear registration in bedpostx ? > And is it recommended ? I am seeing some fibers outside the brain thats > why I am concerned and want to do no linear registration to correct this. > At the moment the commands I am using for linear registration are as > follows: > > flirt -in nodif_brain_subject -ref /Volumes/MAC/DTI_subject/anat_brain.nii.gz > -omat xfms/diff2str.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 > 90 -dof 12 -cost mutualinfo > > convert_xfm -omat xfms/str2diff.mat -inverse xfms/diff2str.mat > > flirt -in /Volumes/MAC/subject/anat_brain.nii.gz -ref > /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -omat > xfms/str2standard.mat -searchrx -90 90 -searchry -90 90 -searchrz -90 90 > -dof 12 -cost corratio > > convert_xfm -omat xfms/standard2str.mat -inverse xfms/str2standard.mat > > convert_xfm -omat xfms/diff2standard.mat -concat xfms/str2standard.mat > xfms/diff2str.mat > > convert_xfm -omat xfms/standard2diff.mat -inverse xfms/diff2standard.mat > > > > Any help is this regard will be extremely appreciated > > > Thanks and best > > Rabia >