To whom it may concern:
I am trying to normalize the MNI152 T1 2mm template to the MNI152 T1 1mm template. I used the following commands to FLIRT and FNIRT the template:
flirt -in MNI152_T1_2mm_brain.nii.gz -ref MNI152_T1_2mm_brain.nii.gz -omat my_linear_transform -out linear_transf_2mm_1mm
fnirt --ref=MNI152_T1_1mm_brain.nii.gz --in=MNI152_T1_2mm_brain.nii.gz --aff=my_linear_transform.mat --cout=my_nonlinear_transform.mat --iout=nonlinear_transf_2mm_1mm
Linear normalization worked, but FNIRT did not output the nonlinear transformation matrix specified by --cout (i.e.'my_nonlinear_transform.mat'). Instead it output an .nii.gz file labeled 'my_nonlinear_transform.mat.nii.gz'. I am not sure why this happened and would appreciate help figuring out how to get -cout to output the correct nonlinear transformation matrix so that I can apply the warp to a set of ROIs.
Thanks in advance,
Anna
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