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MP2RAGE #255

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mathieuboudreau opened this issue Aug 8, 2018 · 3 comments
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@mathieuboudreau mathieuboudreau commented Aug 8, 2018

branch: mp2rage

We might be able to write one, the original author has MATLAB code available to do this on github: https://github.com/JosePMarques/MP2RAGE-related-scripts

He just doesn't have a license, we could open an issue and ask if he'd be willing to upload a license that's permissive that allows for reuse (e.g. MIT).

@mathieuboudreau mathieuboudreau changed the title MP2RAGE module MP2RAGE model Aug 8, 2018
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@mathieuboudreau mathieuboudreau commented Nov 14, 2018

Spoke with Jose Marques by email today, and he gave us the green light to integrate his code into a qMRLab model. I'll get started on it after the VFA interactive notebook gets released, as the MP2RAGE notebook will be the next interactive notebook.

@mathieuboudreau mathieuboudreau self-assigned this Nov 14, 2018
@agahkarakuzu agahkarakuzu added this to the Add MP2RAGE milestone Dec 5, 2018
@mathieuboudreau mathieuboudreau changed the title MP2RAGE model [Mathieu] MP2RAGE Dec 11, 2018
@mathieuboudreau mathieuboudreau changed the title [Mathieu] MP2RAGE MP2RAGE Dec 11, 2018
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@mathieuboudreau mathieuboudreau commented Sep 12, 2019

To do:

  • Copy files from https://github.com/JosePMarques/MP2RAGE-related-scripts into repo
  • Upload data files to OSF
  • Create empty template MP2RAGE model, and make sure it opens.
  • Copy demo script from Marques' repo into MP2RAGE template, and make it run when "Fit data" is clicked.
  • Refactor how data inputs are handled
  • Refactor how options are handled, but still use hardcoded values
  • Create GUI options, but don't replace the hardcoded values in the code yet
  • Assert that the default input options are equal to the hardcoded demo values
  • Replace hardcoded values by passed options values
  • Refactor to handle optional B1 map case
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@agahkarakuzu agahkarakuzu commented Oct 8, 2019

@mathieuboudreau
Difference between T1corrected.nii (B1 corrected, original output, uint16) and T1.nii.gz (B1 corrected in qMRLab, double).

image

Differences may be due to compression and data type. To ensure, fit using orig code and compare outputs in matlab workspace.

  • Do one more comparison
  • Add B1map range control/correction

This is how the mp2rage panel looks like:

image

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