Dear experts,
I have a question concerning the normalization of CBF images into MNI
space. In a first step I registered the T1 weighted image to MNI space
(linear and non-linear) and the images looks quite normal. In the
native space the M0 and perfusion image are also perfect. Furthermore
linear transformation of the M0 to the strucural image worked well.
However, when I warp the M0 and perfusion images into MNI space the
images look a little bit frayed at the edges (or curvy - partly
eroded). I have only 16 slices (not whole brain). Did I make something
wrong?
Here is the code I used.
#lineare transformation of T1
flirt -in ${datapath}/oanat_brain.nii.gz -ref
/opt_prg/fsl/fsl-5.0.9/data/standard/MNI152_T1_1mm_brain.nii.gz -out
${datapath}/oanat_brain_linear.nii.gz -omat
${datapath}/oanat_brain_linear.mat -bins 256 -cost corratio -searchrx
-90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
#non-linear transformation of T1
fnirt --in=${datapath}/oanat.nii
--aff=${datapath}/oanat_brain_linear.mat
--cout=${datapath}/oanat_nonlinear_trans.nii --config=T1_2_MNI152_2mm
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm
--in=${datapath}/oanat.nii --warp=${datapath}/oanat_nonlinear_trans
--out=${datapath}/oanat_warped_structural
#coregister M0 on T1
flirt -in ${datapath1}/native_space/M0image_brain1.nii -ref
${datapath}/oanat_brain.nii.gz -out
${datapath1}/native_space/M0image_reg.nii -omat
${datapath1}/native_space/M0image_reg.mat -bins 256 -cost corratio
-searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6 -interp
trilinear
#apply warping M0 and perfusion
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm
--in=${datapath1}/native_space/M0image_brain1
--warp=${datapath}/oanat_nonlinear_trans
--premat=${datapath1}/native_space/M0image_reg.mat
--out=${datapath1}/native_space/M0_warped_structural
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm
--in=${datapath1}/native_space/perfusion
--warp=${datapath}/oanat_nonlinear_trans
--premat=${datapath1}/native_space/M0image_reg.mat
--out=${datapath1}/native_space/perfusion_warped_structural
Best
Ralf
Ralf Veit PhD
Institute of Medical Psychology and Behavioral Neurobiology
Otfried-Müller str. 47
72076 Tübingen
phone: +49-7071-2987703
fax: +49-7071-295706
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