Did you look to see if the registration worked?
Matt.
On 1/29/19, 10:11 AM, "C. Roman" <[log in to unmask]> wrote:
>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
>
>
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|