What's the voxel size in the rodent data? I've noticed some flaky behavior in the past with TBSS if the voxel dimensions are < 1mm.... Like I am guessing your data is probably 0.1 or 0.2 microns or so..... if that's the case simply multiple everything by 10/edit your headers so the voxel dimensions are greater than one mm.

On Fri, Apr 24, 2015 at 1:13 PM Subscribe FSL Patrick McCunn <[log in to unmask]> wrote:

Hi
I've been attempting to run tbss on rodent data in fsl. I've worked around several of the issues (e.g. bet) and have my fa maps ready to go. When looking at the output files of tbss_1_preproc and tbss_2_reg it seems like everything runs ok but in after the tbss_3_postreg my files (all_FA etc.) are mostly empty or occasionally have a tiny portion of data right in the centre. I've run these on human data and know that the steps are correct and the data is prepared correctly. Does anyone have experience and editing the tbss scripts to work with rodent data?
Patrick