Negative values while calculating tract averaged fixel metrics

[pinghongyeh]

Hi MRtrix experts,

I tried to calculate tract averaged fixel metrics, e.g. diffusivity, but a few tracts had negative mean values of diffusivity. When eye-balling the regions by overlaying the fixel plots of segmented tract and diffusivity map, I did not notice negative diffusivity values within that specific tract ROI (see attached).

Here is steps I used,

1. ‘BINARIZING TRACT FIXEL MASKS’
   for tract in ts_out/{averageresponse}_tck_fixels/*.mif
   do mrthreshold tract {tract//.mif}_bin.mif -abs 1 -force
   done

2. Warp map to template space

   warpfile=find $dwipath/${subject}2${averageresponse}_wmfodtemplate_warp.mif*
   mrtransform dwipath/{metric}.nii.gz -warp $warpfile dwipath/{metric}_${averageresponse}_WMFODs_template.nii.gz -force

3. #Map voxel data to fixels
   voxel2fixel dwipath/{metric}_${averageresponse}_WMFODs_template.nii.gz out_dir/template/{averageresponse}fd $out_dir/template/fixel_stats/metric/ {subject}${metric}.mif -force

4. #Calculating tract averaged fixel metrics
   mrstats $out_dir/template/fixel_stats/metric/{subject}_${metric}.mif -mask ts_out/{averageresponse}tck_fixels/${track_name}bin.mif -output mean > out_dir/template/tractstats/{averageresponse}{metric}/{subject}${track_name}.txt

The mean value was -0.00092223

Thank you.
Ping