Sorry, don´t know why the first thing that shows up is html. Here´s the post.
Hello All,
I have a couple newbie questions regarding the brain extraction and FA map results.
First, several of my images are left with holes or gouges around the exterior of the brain mask after the BET step and I´ve seen responses to previous posts that mention lowering the brain/non-brain %threshold, using voxel-wise regressors to account for these lost voxels, manually creating the mask, etc; what is the best option for someone relatively new to the software to modify these masks? I´m trying to attach an example of one of the faulty masks below.
Second, most of my FA intensity-modulated color maps look fine after reconstructing the diffusion tensors in DTIFIT, but a few have strange red/interhemispheric hyperintensities that are apparent in the sagittal view, usually in parietal Brodmann areas 7 and 19. Any reasons why this is coming up? Could the intensity have been poorly regulated in a previous step? Again, will try to attach a picture.
All files are 4D NIFTI files from T2 weighted images (Siemens 3T).
Thanks.
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