I am trying to prepare data for a voxel-based analysis.
for this purpose, I have to coregister all data to a template.
For now I am using MNI_T1_2mm template provided by FSL
Thus, I have used this script to coregister MPRAGE to T1 template
(this is based on FNIRT manual):
mpr=`$FSLDIR/bin/remove_ext $1`
mpr_brain=`$FSLDIR/bin/remove_ext $2`
flirt -dof 6 -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -in
${mpr_brain} -omat ${mpr_brain}_transf.mat -out ${mpr_brain}_flirted
fnirt --in=${mpr} --aff=${mpr_brain}_transf.mat
--cout=${mpr}_nonlinear_transf
--ref=$FSLDIR/data/standard/MNI152_T1_2mm --imprefm=0 --impinm=0
--config=T1_2_MNI152_2mm
applywarp --ref=$FSLDIR/data/standard/MNI152_T1_2mm --in=${mpr}
--warp=${mpr}_nonlinear_transf --out=${mpr}_warped
Attached is a result from 4 subjects
There is a lot of "play" in different brain areas. Is this the best
what can be done or I did something wrong or I missed something?
Thank you very much for your help
Lazar
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