[Neuroimaging] Reconstruction issues using MAP-MRI model

[Chen Wang (SDS, 120090637)]

Dear Developers,

We are a medical lab from Shenzhen Research Institute of Big Data, China. We are doing an urgent and important research about Intermittent Exotropia, which is a common progressive disease in children.  We need to reconstruct the brain parameters using MAP-MRI model from dipy. However, we met a problem with the reconstruction of the whole brain. We have searched our problem in the forum on github but there isn't any valuable solution. Therefore, we are writing this email to ask for help. The details are shown below.

When we run the example code reconst_mapmri.ipynb (https://dipy.org/documentation/1.7.0/examples_built/07_reconstruction/reconst_mapmri/#sphx-glr-examples-built-07-reconstruction-reconst-mapmri-py), it is good when we use the image fragment data_small [40:65, 50:51]. However, when we run the code on the whole brain, the images of RTOP, RTAP, and RTPP parameters will be wrong, which contain no signals. We have also tried the preprocessing step to add a mask by Brain segmentation with median_otsu<https://dipy.org/documentation/1.7.0/examples_built/04_preprocessing/brain_extraction_dwi/>.ipynb (https://dipy.org/documentation/1.7.0/examples_built/04_preprocessing/brain_extraction_dwi/), but it does not work. The correct and wrong outputs are shown below.

Wrong output:

[cid:f70f8de6-953a-4336-ae46-c7a16ce692fe]
Correct output:
[cid:72682e07-4f6c-4d32-a688-f6b484447e53]
We'd highly appreciated it if you could help us solve this problem. Thanks a lot! Looking forward to your reply!
Best wishes,
Chen Wang

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