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BrkRaw / brkraw

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
https://brkraw.github.io
GNU General Public License v3.0
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Brkraw CLI for bruker recon of simple cartesian sequences (FLASH, MGE, RARE) #157

Open timwahoo opened 7 months ago

timwahoo commented 7 months ago

Is your feature request related to a problem? Please describe. Offline reconstruction is an important part of data control for Scientist since there are many various methods for coil combination, phase processing, and image de-noising.

Describe the solution you'd like A command line interface that will reconstructed simple Bruker Cartesian sequences within a dataset as two NIFTI files (one with magnitude information and one with phase information). Although this solution does not encompass all possible sequences, it is a start for using brkraw as an intermediate tool for other post processing methods such as QSM and SWI.

Describe alternatives you've considered I've thought about including ISMRMRD format for its connection with gadgetron. However, I have not been successful in getting it to work locally yet.

dvm-shlee commented 7 months ago

@timwahoo Have you got a change to test on BOLD EPI image as well? If not, could you help to test it out? I can share some data if you available, Thank you!

timwahoo commented 7 months ago

Hi @dvm-shlee,

I could look into it, I do not have any good examples of EPI datasets available. The best example I currently have is from Maxime (Weizmann folder) but that is a custom double-sampled EPI and can't be used for a catchall EPI reconstruction protocol.

dvm-shlee commented 5 months ago

Hi @timwahoo,

I hope you're enjoying ISMRM! I wanted to give you a heads-up that the plugin architecture is now integrated. You can check out a sample here: Brkraw-snippets.

Essentially, if you create a class with the get_nifti1image() function, it can be launched directly from the tonifti module. There’s no need for installation; the module searches the GitHub repo and downloads the necessary snippets for conversion.

I'll provide more details later, but I wanted to get this on your radar in case you're interested. Given that your code is already optimized for the new API, a little organization could enable you to build your own plugin. Perhaps you could create your version of the recon and generate a pull request on GitHub (or you can just create your own repo under your account, and put repo address to Brkraw's config file, by adding same block as I did it for brkraw-snippets repo. I've also included metadata specifications for the plugin, so author details, license, and citation information can be included, if you like.

Let's keep in touch, and please reach out if you have any questions about migrating your code to this new plugin system.

dvm-shlee commented 5 months ago

Hi @timwahoo,

I'm almost finished with the core API module and will soon be transitioning to developing the new command-line interface. Consequently, the plugin module will be stabilized shortly. I plan to integrate your reconstruction code into the plugin by early next week. Could you assist with some testing or help polish the code when it's ready? Thanks!

timwahoo commented 5 months ago

Hi @dvm-shlee,

Sounds great. I should be free to work on this next week as well. Let me know how I can assist!