hello everyone,
I am a Master thesis student working on DTI .... I have a problem transforming images standard to functional space and functional to standard space for me FLIRT and FNIRT are working fine the images are well registered but the problem is applywrap. I am getting a distorted image of Functional_standard space and standard_functional space after applywrap.
plz can anyone help ...any suggestion would be appreciated...I have pasted my code below
/usr/share/fsl/5.0/bin/flirt -in T1_brain.nii.gz -ref /usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz -out T1_brain_lin2MNI -omat T1_brain_lin2MNI.mat -bins 256 -cost corratio -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -dof 12 -interp trilinear
/usr/share/fsl/5.0/bin/fnirt --in=T1_brain.nii.gz --aff=T1_brain_lin2MNI.mat --ref=/usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz --config=/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_2mm.cnf --cout=coef_T1_brain_to_MNI152 --iout=fnirted_T1_brain
/usr/share/fsl/5.0/bin/flirt -in dti_FA.nii.gz -ref fnirted_T1_brain -out dti_FA_affine2T1 -omat dti_FA_affine2T1.mat -bins 256 -cost corratio -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -dof 12 -interp trilinear
/usr/share/fsl/5.0/bin/convertwarp --out=dti_FA_warp2MNI.nii.gz --premat=dti_FA_affine2T1.mat --warp1=coef_T1_brain_to_MNI152.nii.gz --ref=/usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii
/usr/share/fsl/5.0/bin/applywarp --in=dti_FA.nii.gz --out=dti_FA_nlin2MNI --ref=/usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz --warp=dti_FA_warp2MNI.nii.gz
/usr/share/fsl/5.0/bin/convert_xfm -omat T1_brain2FA.mat -inverse dti_FA_affine2T1.mat
/usr/share/fsl/5.0/bin/invwarp --warp=dti_FA_warp2MNI.nii.gz --out=MNI152_warp2FA.nii.gz --ref=fnirted_T1_brain
/usr/share/fsl/5.0/bin/applywarp --in=/usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz --ref=dti_FA.nii.gz --out=MNI152_nlin2FA.nii.gz --postmat=T1_brain2FA.mat --warp=MNI152_warp2FA.nii.gz
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