Hello experts,
I want to transform a mask from standard space to structural space and I have some questions.
The steps I was going to take were:
1) do BET on structural image
2) do FLIRT: flirt -in MNI152_T1_2mm_brain.nii -ref struct_brain.nii.gz -omat flirted_MNI.mat
3) do FNIRT: fnirt --in MNI152_T1_2mm.nii --ref struct.nii.gz --aff flirted_MNI.mat --config ???? ---cout coef_MNI_to_struct --iout fnirted_mask
4) transform the mask: applywarp -i standard_mask -r struct_brain -coef flirted_MNI.mat -out struct_mask
5) threshold new mask with fslmaths
First of all: are these the right steps to take? Am I forgetting any important steps or arguments?
What config file should I use? Can I use the standard one that goes in the other direction (T1_2_MNI152_2mm)?
Thank you for your input
Nele
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