Blog b1_afi

[jvelazquez-reyes]

@mathieuboudreau I opened this pull request to discuss about the Jupyter Notebook for the blog. First, I took a JN of the qMRLab/t1_notebooks project as a template and I customized it for the b1_afi method. I tested the ActualFlipAngleImaging.ipynb locally, the method and its functions to run the simulations are working, and the interactive plots were displayed with no problems.

For Binder, I added sos-r, matplotlib and I updated the sos, sos-notebook and plotly to solve some Requirement.parse errors. I temporarily changed a couple of CLI instructions in the Dockerfile regarding git clone, as the branches b1_afi and blog_afi are not merged into master. However, an error error: 'b1_afi' undefined near line 7 column 16 is still occurring and I suspect it is about this git checkout in line 69, which I'm not sure how to solve it.

https://github.com/jvelazquez-reyes/t1_notebooks/blob/blog_afi/Dockerfile#L65-L74

[mathieuboudreau]

@jvelazquez-reyes are you sure you are checking out the right commit number? Looking in the commit history of the AFI branch(https://github.com/qMRLab/qMRLab/commits/update_2.5.0), I don't see that commit number, which may explain why it can't find the b1_afi module.

[jvelazquez-reyes]

Hello @mathieuboudreau, I wasn't sure what commit number should be but I git checkedout the latest commit of the AFI branch (https://github.com/qMRLab/qMRLab/commits/update_2.5.0), - it made sense- and it solved the b1_afi undefined issue.

Now, I ran into a new issue regarding Figure 8 (ONLY) to display the dataset and an example of a B1 map (https://github.com/jvelazquez-reyes/t1_notebooks/blob/blog_afi/afi_blog/ActualFlipAngleImaging.ipynb). The data is successfully downloaded from the OSF. I loaded the data using load_nii_data but when I try to run the b1_afi module a struct has no member b1_afi error occurs, which is strange as I'm able to call b1_afi module and its function to display previous plots. I tried manually loading MAT files but the outcome is the same. Also, I'm struggling to transfer the data (AFI data) from Matlab/Octave to Python using %get. I got this error AFIData1 does not exist even though with the command whos I can see that data is there.

Please @mathieuboudreau, @agahkarakuzu, @TommyBoshkovski, any hint you could give would be much appreciated. Thank you!

[mathieuboudreau]

Hi @jvelazquez-reyes ,

Sorry for the delayed response - we have the ISMRM conference going on this week, and I've been very busy leading up to it and up until mid-next week. After that I will have more time to look into this. Please send me a reminder in two weeks if I haven't responded yet.

Best,

Mathieu