Dear Freesurfer experts
I finished TRACULA's trac-all steps. Then I'd like to transform all DTI pathways to MNI space.
Are there any commands in freesurfer or any external neuroimaging softwares.
My scripts did not provided no transformation to MNI space.
#bet /Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz /Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz
#flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in /Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz -omat /Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat
fnirt --in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz --aff=/Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat --cout=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf --config=T1_2_MNI152_2mm
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm --in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz --warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf --out=/Users/anal/RH_nml/FS/01/mri/orig/warped_001.nii.gz
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm --in=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/path.pd.nii.gz --warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf --premat=func2struct.mat --out=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/warped_fmajor.nii.gz
Sincerely
Woo-Suk, Tae
Seoul, Korea
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Woo-Suk, Tae Ph.D. Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: wstae@korea.ac.kr, woosuk.tae@gmail.com,
woostae@gmail.com
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