Fixel Threshold

Dear Experts,

I am seeking fome clarification on how to threshold the fixel mask to 500,000 which is part of the 7th step of the FBA.

Is this done by simply using the fixelthreshold command?

Where in the command below should the 500,000 be specified?

fod2fixel -mask <input_analysis_voxel_mask> <input_fod_template_image> -peak <output_temp.msf>
fixelthreshold <input_temp.msf> -crop 0.2 <output_analysis_fixel_mask.msf> -force
rm <temp.msf>

Thanks in advance for the help,


Hi James,
Assuming you are using the *.msf files for fixels, you can use fixelstats to check how many fixels are in the file. You may then need to go back and try a different threshold to reduce the number.

Note this number is only an upper limit. Depending on your resolution, you may have a perfectly good (i.e. covers all of white matter) fixel mask with only 250,000 fixels.