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spinal-cord-7t / coil-qc-code

7T Spinal Cord Coil QC Analysis Code
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Data processing code for B1+ efficiency #11

Closed Kyota-exe closed 7 months ago

Kyota-exe commented 7 months ago

In this PR, I will write all the processing/plotting code to generate the figures related to B1+ efficiency mentioned in #7. The current data_processing.ipynb is a work in progress, and only generates for now a graph of the standard deviation of B1+ efficiency, which will soon be replaced by a graph of the inter-quartile range (IQR) across slices.

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evaalonsoortiz commented 7 months ago

I just ran the notebook locally. This is a good start. I added an additional figure (which I'll refer to as Fig1 here) which I think is helpful for visual assessment of results:

Fig1 image

The SC mask does not span the same levels for all subjects, as you can see in the Fig1 above. This means that for the IQR plot (see below) isn't really a fair comparison.

Fig2 image

We should restrict the analysis to the same SC levels for all subjects. For this we will need a vertebral levels file.

evaalonsoortiz commented 7 months ago

I propose that we deal with the SC labels in another issue/PR and move forward with merging this one.

jcohenadad commented 7 months ago

That PR was merged with the notebook that included the results and the figures. As I mentioned in https://github.com/spinal-cord-7t/coil-qc-code/issues/5, binaries and any notebook outputs should not be added to the git history. It will make cloning of the repository slower, and the repository will increase in size as new binaries are pushed to the repos.

evaalonsoortiz commented 7 months ago

That PR was merged with the notebook that included the results and the figures. As I mentioned in #5, binaries and any notebook outputs should not be added to the git history. It will make cloning of the repository slower, and the repository will increase in size as new binaries are pushed to the repos.

Fixed