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neuroimagen:2mni

FSL space transformations

transforms to to standard space (FDG, DTI, PIB)

1. - Functional Images (FDG, PIB, etc)

Registering functional data to MNI152 (via structural scan)

$ bet my_structural my_betted_structural

$ flirt -ref my_betted_structural -in my_functional -dof 7 -omat func2struct.mat

$ flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat

$ fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm   

$ applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_functional --warp=my_nonlinear_transf --premat=func2struct.mat --out=my_warped_functional

2.- DTI

Registering FA-image to FMRIB58

$ flirt -ref ${FSLDIR}/data/standard/FMRIB58_FA_1mm_brain -in my_FA -omat my_affine_transf.mat

$ fnirt --in=my_FA --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=FA_2_FMRIB58_1mm
$ applywarp --ref=${FSLDIR}/data/standard/FMRIB58_FA_1mm_brain --in=my_FA --warp=my_nonlinear_transf --out=my_warped_FA

$ vecreg -i dti_V1 -o warped_V1 -r /usr/local/fsl/data/standard/FMRIB58_FA_1mm -w my_nonlinear  <----------- !!!!!!

3.- From struc to MNI

$ flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in uk0101_brain -omat uk0101_affine.mat

$ fnirt --in=uk0101_struc --aff=uk0101_affine.mat --cout=uk0101_nonlinear  --config=T1_2_MNI152_2mm

$ applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=uk0101_pet_in_struc.nii.gz --warp=uk0101_nonlinear --out=uk0101_pet_inMNI
neuroimagen/2mni.txt · Last modified: 2020/08/04 10:58 (external edit)