preprocessing.ipynb script error and T2 Maps

sbonaretti / pyKNEEr

An image analysis workflow for open and reproducible research on femoral knee cartilage

https://sbonaretti.github.io/pyKNEEr/

GNU General Public License v3.0

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preprocessing.ipynb script error and T2 Maps #9

Open JosCoelho opened 3 years ago

JosCoelho commented 3 years ago

Hello. My name is José and I am PhD student studying the decay of the T2 and T2 * signal of cartilage in patients with ligament injury. Using this software, after running the script “preprocessing.ipynb”, in the end always gives me an error using the images in the “Demo” folder or my own images:

Will there be a possibility to elucidate what I am doing wrong?

Also, in this thead: https://github.com/sbonaretti/pyKNEEr/issues/6#issuecomment-674742993 you said that PyKneer uses only DESS sequence to calculate the T2 Maps. Can it work with Fast Spin Eco Multi Eco T2 sequence? And could it be done with T2* Multi Eco sequence?

Thank you for you attention.

sbonaretti commented 3 years ago

Hi José, Sorry for my delay, and thanks so much for being this patient!

Please, change the command to:

show_fitting_maps(view_modality = 0)

The parameter view_modality can get value 0 or 1. One is for static visualization, the other for interactive visualization.

I am not an expert in MR acquisition, so I am not sure I can provide a correct answer to your second question. I guess I'll have to refer you to the literature for that.

Hope it helps!