Remove fixels with value 0 from fixelmask

Dear experts,

After using tck2fixel, I am trying to see how many fixels I have in my tck-weighted fixel mask. How could I do this? I just want to erase the fixels with value 0 from the mask.

Some useful commands to do such a thing (fixelthreshold , fixelstats or fixelcalc), are deprecated and not available on the last version.

Thank you for your help!!

I’m pretty sure you can achieve this with fixelcrop, e.g.

fixelcrop template_fixel_directory tck_mask_fixel_directory/tck_mask.mif template_fixel_directory_cropped

then you can run mrinfo on any file in the resulting cropped fixel directory to get the size.

Looks like @anege came across the solution to this issue, but the text got piped to the wrong stream deep in the depths of the Discourse server where nobody can see it :crazy_face:

With the fixel directory format, because each fixel data file is just a 1D image file, many “workhorse” MRtrix3 commands are applicable, including mrthrehsold. So applying a threshold of e.g. 0.5, and then feeding the result as the -mask option of mrstats, should provide the number of super-threshold fixels in the “count” output.

The fixelcrop option suggested by @rgrazioplene should give the same answer, but is doing a bit more work to get there: It creates a new fixel directory, where only those fixels in the input directory that have a value of 1 in the mask (e.g. super-threshold as determined by mrthreshold) are included in the output fixel directory; those fixels that have a value of 0 in the mask are omitted entirely. So the number of fixels present in that directory will correspond to the number of fixels that had a value of 1 in your mask; but you also have a new fixel directory containing only those fixels, which you may or may not want depending on context.