Adding brkrecon CLI and minor updates #158

timwahoo · 2024-03-26T21:53:10Z

Addressing #153, #154, #157

Changes proposed in this pull request:

brkrecon CLI command has been updated to use a tonii function similar to brkraw tonii to reconstruction FLASH, MGE, and RARE sequences to generate two nifti files (orientations for PV360 are accurate to references generated by brkraw)
recoSigpy.py has been added for compressed sensing (this is still in early stage integration)
minor update in main_win.py to also look for unique PvDataset ending in file system
new test scripts for different dataset obtained from the PCI community for external validation

@BrkRaw/Bruker

minor changes to recon

Tim and others added 29 commits February 1, 2024 12:24

clean up code

3d355b4

Merge branch 'BrkRaw:main' into main

2b6a194

Merge branch 'BrkRaw:main' into post_processing

8d5ba72

fixed save individual coil image

2762416

fixed indivdual coil save

0bca426

Merge pull request #2 from timwahoo/post_processing

1352b90

minor changes to recon

minor fix to correct for saving correct coil

9fac019

Merge branch 'main' of https://github.com/timwahoo/brkraw

5062114

Merge branch 'BrkRaw:main' into main

919eb6a

Commit for GUI

cc783c4

ifftn correction

7e65a9c

latest recon edits

8eebb6d

updated recon for pv6 and 7

1ab3a47

fixes

e949ed3

fixes for pv6/7 recon

6311fd5

recon code cleanup

bcc7658

recon tests scripts

b1a927b

code cleanup

7c56786

remove print

ef2c99c

updated brkrecon for simple recon using command line

a899e6c

brkrecon edits

264e2b5

added general save function

30b5134

remove debug print

22905db

minor edits

b9fe39f

corrected orientations for 360 and lower versions

3872e32

remove print statements

3645a68

edits to brkrecon

43fc1c6

remove print

50ba544

update brkrecon -f help info

6bfd95f

dvm-shlee merged commit c7f654a into BrkRaw:main Mar 27, 2024
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