Population Mask Over-crop

Dear MRtrix experts,

I am doing a population analysis with more than 100 subjects and the population mask turned up to be over-cropped since my research team only have single shell data which is (1s b=0 and 64s b=1000).

For my case, it over-cropped part of the corpus-callosum and thalamus.

Do we have any better solution or threshold can be set for this?


Hi @choy950721,

When I saw the term “over-cropped” I thought you would be describing something along the lines of the population mask containing only the centre of the brain and not including the outer extremities of the brain, which can occur in cohorts with a lot of motion. However the CC and thalamus are hardly “peripheral” structures; so it sounds like there is a different issue occurring here.

Can you provide an image that demonstrates the issue?

The population mask will only omit voxels where there is at least one subject where the voxel is not within the brain mask. So I would expect that the issue is in fact that one or more subject masks are erroneous, and the population mask is in fact a downstream symptom of such. Currently the “threshold” that is set for this is that all subjects must have FOD data available; while this could theoretically be changed, it’s not a simple matter of only deviating from the documentation by changing some numerical value. So I would advise finding the source of the issue rather than falling down that rabbit-hole.


I second what Rob said: I’d fix the input masks if possible and re-runpopulation_template.

population_template uses masks to define areas that drive registration, the template itself is generated using all data, irrespective of masks. If you can live with subjects potentially not being well aligned in areas outside the (erroneous) mask you could just refine the template masks.

In case you have the temporary directory of population_template, you can use mrmath masks_transformed/* sum - | mrview masks_transformed/* -overlay.load - -overlay.opacity 0.2 to check all masks quickly. If you only have the transformations, not the temporary directory, you can transform the input masks to template space:
mrtransform subject_mask.mif -template template.mif -warp_full warp.mif masks_transformed/subject_mask.mif -interp nearest

To recreate the template mask, use mrmath masks_transformed/* min - | maskfilter - median - | maskfilter - dilate -npass 5 new_template_mask.mif or replace min with median if that is what you want to do.