Hello,
I have a follow-up question to this string, please.
I am currently using the following to transform my T2 FLAIR into b0 space, with the intention of using the transformation matrix to transform a lesion map into diffusion space. However, after I run applywarp, the warped T2 is completely empty.
flirt -ref avg_b0.nii -in T2_FLAIR.nii -omat my_affine_transf.mat
fnirt --ref=avg_b0.nii --in=T2_FLAIR.nii --aff=my_affine_transf.mat --cout=nonlinear_transf
THEN, to apply the transform:
applywarp --ref=avg_b0.nii --in=T2-FLAIR.nii --warp=nonlinear_transf --out=warped_T2_FLAIR
However, after doing this, the warped_T2_FLAIR image is completely empty.
My second question- Once I figure out the above, can I just apply the above transformation matrix to my lesion map by running the following?
applywarp --ref=avg_b0.nii --in=lesion_probaility_map --warp=nonlinear_transf --out=warped_lesion_map
Thank you so much for your time!
Cristina
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|