I’m sorry if this doubt is too basic, but I still can’t understand this error.
Basically, I am transforming one image to the space of another images like this:
flirt -dof 6 -cost normmi -in $path_S2/data_mnb0.nii -ref $path_S1/data_mnb0.nii -omat $path_S1/T_fsl.txt
transformconvert $path_S1/T_fsl.txt $path_S2/data_mnb0.nii $path_S1/data_mnb0.nii flirt_import $path_S1/S2_2_S1_transformation.txt -force
mrtransform -linear $path_S1/S2_2_S1_transformation.txt $path_S2/data_mnb0.nii $path_S1/data_mnb0_S2_2_S1.nii -template $path_S1/data_mnb0.nii -interp cubic -force
It works ok for almost all cases, but then for some subjects, with the last line I get this error message:
“contains non-rigid transform - qform will not be stored.”
I don’t understand why it should have a non-rigid transform if I am asking it to be made with only 6 degrees of freedom…
I saw this topic, so maybe it just has to do with the way the data is stored and not the transformation itself?
Thank you in advance!