T1w intensity harmonization (or intensity normalization)

[oesteban]

I've been entertaining this idea for a while, and I think that it would make our measures a lot more homogeneous across sites.

These two refs. could give me a start:

• http://ceur-ws.org/Vol-347/p036.pdf
• http://ieeexplore.ieee.org/document/836373/

Other refs.:

• http://www.eyemaginary.com/Rendering/AutomaticHistogramWarping.pdf
• http://ieeexplore.ieee.org/document/537491/

[chrisgorgo]

https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dUnifize.html

[chrisgorgo]

These guys are doing 3dUnifize after N4BiasFieldCorrection - https://github.com/jlohmeier/atlasBREX.

[oesteban]

I'd run it before and after. Like they laterally recommend in their docs

…

On May 9, 2017 16:35, "Chris Filo Gorgolewski" ***@***.***> wrote: These guys are doing 3dUnifize after N4BiasFieldCorrection - https://github.com/jlohmeier/atlasBREX. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#489 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAkhxpcm8NKnINHXESj8H-AQbeUcCXvKks5r4Pg0gaJpZM4NSd0A> .

[chrisgorgo]

3dUnifize seems to be removing the bias field (see https://youtu.be/LxApX0Ijg5w) running it before N4 might impair the matrics that were suppose to measure bias field.

[oesteban]

I was referring to 3dSkullStrip with the before/after. See implementation :)