Dear FSL list,
I'm trying to generate the subject atlas mask in the DTI native space from two different atlases. One of them (AAL) is in MNI space, but the other one (resting-state Shen) is in Talairach space.
For AAL my commands are as follows:
1. flirt -ref M01_structural_brain.nii.gz -in dti_fin_b0.nii -out FA2T1_brain -omat FA2T1.mat
2. flirt -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -in M01_structural_brain.nii.gz -omat my_affine_transf.mat
3. fnirt --config=$FSLDIR/etc/flirtsch/T1_2_MNI152_2mm.cnf --in=M01_structural.nii --aff=my_affine_transf.mat --cout=my_nonlinear_transf
4. convert_xfm -omat T12FA.mat -inverse FA2T1.mat
5. invwarp --ref=M01_structural.nii --warp=my_nonlinear_transf.nii.gz --out=nonlinear_MNI2T1
6. # AAL in diffusion native space:
applywarp --ref=dti_fin_b0.nii --in=aal2.nii --warp=nonlinear_MNI2T1 --postmat=T12FA.mat --out=AAL_FA_native_space --interp=nn
A.- I think that this is correct. Isn't it?
B.- But I tried several commands with resting-state atlas SHEN (fconn_atlas_150_2mm in Talairach space) and I still have not found a solution.
Which steps do I need to perform in order to obtain the transformation with Shen atlas?
Any comments will be appreciated.
Thanks in advanced,
Anira
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