Hello,
I am trying to register my FA image to my anatomical image using flirt so that I can inverse the .mat file and register a co-registered segmented image to the FA image with the following command.
flirt -dof 6 -interp nearestneighbour -in /Volumes/DANIEL/ROI_Analysis/${subj}.${cond}.dti_FDT_FA.nii.gz -ref /Volumes/DANIEL/ROI_Analysis/${subj}.${cond}.anat_3d_final_skull_strip.nii -out /Volumes/DANIEL/ROI_Analysis/${subj}.${cond}.registered.nii -omat dti2anat.${subj}.${cond}.mat
convert_xfm -omat inverse_dti2anat.${subj}.${cond}.mat -inverse dti2anat.${subj}.${cond}.mat
flirt -dof 6 -interp nearestneighbour -in /Volumes/DANIEL/ROI_Analysis/${subj}.${cond}.aseg-in-anat-native.nii.gz -ref $/Volumes/DANIEL/ROI_Analysis/${subj}.${cond}.dti_FDT_FA.nii.gz -applyxfm -init inverse_dti2anat.${subj}.${cond}.mat -o /Volumes/DANIEL/ROI_Analysis/${subj}.${cond}.aseg-in-dti-native.nii.gz
However, I get this error
flirt -dof 6 -interp nearestneighbour -in /Volumes/DANIEL/ROI_Analysis/AES120.Ex.dti_FDT_FA.nii.gz -ref /Volumes/DANIEL/ROI_Analysis/AES120.Ex.anat_3d_final_skull_strip.nii -out /Volumes/DANIEL/ROI_Analysis/AES120.Ex.registered.nii -omat dti2anat.AES120.Ex.mat
convert_xfm -omat inverse_dti2anat.AES120.Ex.mat -inverse dti2anat.AES120.Ex.mat
Illegal variable name.
Also, the output of the registered FA image to the anatomical is less aligned than the origional FA image.
I tried running fslreorient2std but besides this I am unsure what the issue is with the registration and outputs.
Best,
Daniel
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