Hi Mathew,
Thank you for your reply.
I uploaded 3 different masked FA images. They were created via dt_recon and masked based on T1 white matter segmentation.
I have tried using them directly in tbss however I have run into the problem described above.
The only way I can seem to improve the tbss performance is by running flirt before running tbss.
flirt -interp nearestneighbour -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -in /Volumes/DANIEL/dti_FDT_FA_freesurf/${subj}.${cond}.nii.gz -ref $FSLDIR/data/standard/FMRIB58_FA_1mm.nii.gz -omat ${subj}.${cond}.flirt.mat -out ${subj}.${cond}.nii.gz
when I tried to implement flirt -interp nearestneighbour -searchrx -180 180 -searchry -180 180 -searchrz -180 180 into the source code of tbss_2 as we discussed in a separate forum discussion it still did not work.
Looking forward to hearing what your thoughts on the FA data I uploaded is!
Best,
Daniel
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