Bad effect of population_template_mask


It’s me again :sweat_smile:, after I registered the population_template.mif to the FMRIB58_FA.nii.gz, I then performed the step 10 and step 11 accroding to the document. Then …the effect is not good. The mask loses some occipital regions of the template. Yet before I register the template to MNI, the mask resulted from it looked good.

I thought it may be because the voxel size is different between the population_template.mif and the subject_mask.mif, but after I regrided the subject_mask.mif to the voxel grid of the population_template.mif, the effect didn’t get better.

By the way, because most of the patients in my dataset often have many lesions (e.g. edema), the generated masks are bad, in case of losing some brain regions, I passed the dilated -npass 6 masks to the mrmath -min

Do you have any solution to this? Thanks in advance.


Hello, @maxpietsch

After saw your reply in other post, I replace the mrmath -min with mrmath -median, and it works nice. But I’m a bit worried about this change, since the document doesn’t say that users can select other options when mrmath, and for those papers I’ve read about FBA, they all follow the traditional pipeline which apply the -min. Therefore, I’m confused is there rational to use the mrmath -median when generating the template mask?

Here is the effect generated by the -madian:

Looking forward to your reply, and thank you in advance.