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tkkarjal / magia

Automated brain PET analysis pipeline
https://doi.org/10.3389/fninf.2020.00003
MIT License
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A question about impicit masks in Logan fit #102

Closed SoodehMoallemian closed 7 months ago

SoodehMoallemian commented 3 years ago

Hi all,

For technical reasons we are using only magia_logan_image.m function, mainly because we use reference region instead of blood sampling as the input function.

We also use Ecat HR+ with fbp reconstruction, which leads to a lot of negative values and NANs in first frames. In magia_logan_image.m function, you apply a mask filtering the negative, 0s and NANs, which is too strict for us, removing almost all image. Unfortunately we can't share the images for confidentiality.

For us, we see two solutions:

  1. feed only frames after t*, but it will reduce the values of your Y variable, we guess it should not affect Vt but will reduce intercept
  2. Use magia_fit_logan.m directly, applying only our pre-calculated brain mask.

Could you suggest the best way to proceed, please?

Thanks, Soodeh

joupes commented 7 months ago

Hi, sorry for very late response! I'd suggest the second option.