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New echocombine #22
Merged
kschan0214
merged 8 commits into
kschan0214:new_echocombine
from
korbinian90:new_echocombine
Aug 3, 2021
Merged
New echocombine #22
kschan0214
merged 8 commits into
kschan0214:new_echocombine
from
korbinian90:new_echocombine
Aug 3, 2021
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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 :) |
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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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.