Hi
I just wanted to double check something before running tbss_non_FA. I want to run the script on an individual subject level. After the registration and after creating and masking all AD_to_target into a 4D image I am about to run
${FSLDIR}/bin/tbss_skeleton -i ${PATH_TO_TARGETS}/mean_FA.nii.gz -p "$thresh" ${PATH_TO_TARGETS}/mean_FA_skeleton_mask_dst.nii.gz ${FSLDIR}/data/standard/LowerCingulum_1mm ./masked_FA_to_target/"$masked_img" ./skeletons_MD/"$skeletons" -a ${all_MD}/all_MD -s ${PATH_TO_TARGETS}/mean_FA_skeleton.nii.gz
Considering that all_FA (masked) is a 4D image derived from merging all FA_to_target files it should be correct to simply replace this with the corresponding individual masked FA_to_target image, wouldn`t it? Also is it necessary to provide an alternative 4D image (-a option) in this case?
Thank you.
Best,
Rali
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