Intensity normalization in fixel-based analysis

1

Dear all,

I am currently using the following guide for my fixel-based analysis of DWI data of stroke patients:
https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mt_fibre_density_cross-section.html

The intensity normalization (intensitynorm) has been omitted in this guide, while it was previously present in a guide for preprocessing of quantitative analyses (including FBA):
https://mrtrix.readthedocs.io/en/0.3.16/workflows/DWI_preprocessing_for_quantitative_analysis.html

Is there a specific reason why the intensity normalization has been removed from this guide?

It makes sense to me to include this step in the preprocessing of my FBA data.

Thank you in advance,

Jord

2

Hi,

The step is still performed, but later on in the pipeline and with another command: mtnormalise

Best regards,

Manuel

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3

Dear Manuel,

I see. But in the previous intensity normalization step the intensity is normalized across subjects. In the new mtnormalise, the normalization is performed for each dataset seperately, which made me think a different type of normalization is performed. Could you elaborate on this?

Jord

4

Hi,

There is a recent post here explaining how mtnormalise works. I hope this helps.

Best regards,

Manuel

1 Like
5

Dear Manuel,

Thank you!

Jord