Hello, I have skull-stripped anatomical T1w images and co-registered volume segmentation in this space. I also have post eddy corrected FA images. I would like to register the segmentation into the FA map native space. To do this I wanted to use epi_reg to register the FA image to the T1w image and then inverse the registration of the segmented image back to the FA map.
I am trying this using this command
epi_reg --noclean --epi=${subj}.${cond}.dti_FDT_FA.nii.gz --t1=${subj}.${cond}.anat_3d_skull.nii --t1brain=${subj}.${cond}.anat_3d_final_skull_strip.nii --out=${subj}.${cond}.registered.nii.gz
I get two .mat files init_registered.mat and registered.mat.
I was trying to figure out what each of these .mat files represents?
I assume once I know which .mat file I need to inverse I should use convert_xfm and then use the inverse .mat file in
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
I am trying to figure out which .mat file should go in the -init flag?
Also, does it make sense to use epi_reg somehow for the transformation back instead of using flirt? I have only seen the documentation for specifying the registration matrix .mat file in the flirt command?
Thank you for any advice or suggestions you can provide!
Best,
Daniel
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