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kschan0214 / sepia

Matlab GUI pipeline application for quantitative susceptibility mapping (QSM)
MIT License
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New echocombine #22

Closed korbinian90 closed 2 years ago

korbinian90 commented 2 years ago

Hi Kwok,

This pull-request includes romeo phase unwrapping and the romeo total field calculation option. I requires ROMEO version v3,2.4 (or future releases, which should be compatible) https://github.com/korbinian90/ROMEO/releases

I included the option to use the romeo mask inside sepia. This just replaces the mask in headerAndExtraData. It works but may not be the best way to do it. Also the mask cannot be saved this way.

Implementation detail: Romeo requires temporary storage as the files are first written to disk, then romeo is called and produces output files on disk. The temporary storage is in the default OS tempdir, created by fullfile(tempdir, 'romeo_tmp'). As I didn't find a way to access the output directory for SEPIA, I couldn't write romeo outputs there. The temporary folder is created and deleted at the end.

Thanks again for adapting SEPIA to allow custom echo combinations! And please let me know, if there are some aspects that I could improve.

kschan0214 commented 2 years ago

Hi Korbinian,

I merged the pull request. The ROMEO panel looks nice and neat!

After some testing, I fixed the following compatible issues between ROMEO and SEPIA in the Wrapper_TotalField_ROMEO.m

All the changes are available in the dev branch (the new_echocombine branch will soon be deleted as the feature development is done). You can see if you agree on these changes when you have time :)

korbinian90 commented 2 years ago

Hi Kwok!

Thanks for these changes to make the output compatible! I totally agree with all of those. These were oversights on my part.

Cheers, Korbinian

Am Di., 3. Aug. 2021 um 19:15 Uhr schrieb Kwok-Shing Chan < @.***>:

Hi Korbinian,

I merged the pull request. The ROMEO panel looks nice and neat!

After some testing, I fixed the following compatible issues between ROMEO and SEPIA in the Wrapper_TotalField_ROMEO.m

  • convert unit of TE from second in SEPIA header to ms in the parameters variable of ROMEO
  • invert the N_std variable by 1, as the N_std should have higher values in noisy region (opposite of SNR map)
  • convert the unit of TotalField from Hz to radHz, as the default output unit of the echo combine method wrapper
  • set the NaN (if any) in TotalField to 0

All the changes are available in the dev branch (the new_echocombine branch will soon be deleted as the feature development is done). You can see if you agree on these changes when you have time :)

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