Hello,
After running tbss_3_postreg -S, we are having the problem of the all_FA and mean_FA images being masked too severely. All the FA images up until this point of analysis seem to only have very minor "cuts" - missing tissue is minimal. We are analyzing data from an older, patient population so we ran the registration using the -n flag so that all FA images get aligned to one another, the most representative image is selected, and then all other images are aligned to the target in MNI space. Each FA_to_target image looks ok, but when concatenated together in all_FA and averaged in mean_FA, this is where we see the drastic masking.
Is it possible that the large areas of missing tissue are a result of all the smaller, less serious areas in each individual FA image? Is there anything else that could effect this problem?
Furthermore, since the target_to_MNI152.nii.gz is fine, is there any way we can force the program to use it as a mask for the subsequent outputs?
Finally, does a different level of "cuts" in the tbss_1 step affect the warp/normalization result for each subject? Thanks for the help!
Sara
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