shimming-toolbox / shimming-toolbox / 11938854754

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Add CLI to combine text files (#550)

* Add CLI to combine coefficients of multiple shims

* Reverse f0 for GE, move reordering of GE function to the root of the file

* Add BRAVO sequence to dcm2bids config file

* In combine_shim_coefs, add option to reverse slice order, reorder 2nd order and scale 1st order

* Fix test issues comming from incompatibility with fsl bet2 (#554)

* test

* change link

* dipplay version True

* Fix version of sphinx_rtd_theme

* Ab/compute sig rec (#555)

* modify signal loss maps caluculations

* change mask for saved file

* clean up

* Fix thickness parameter

* fix tests

* Fix default dcm2bids config file not existing on Windows installation (#556)

* Move config file in shimming toolbox directory. Also add to the dcm2bids config file

* Fix BET version test

* Also add to windows install

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Co-authored-by: 4rnaudB <55560824+4rnaudB@users.noreply.github.com>

* Add required code for RTD before they migrate to addons (#552)

* Update dcm2bids config file for Philips and output JSON sidecar for the calculated field maps (#559)

* Add mprage

* Output json file for calculated b0 fmap after shimming

* Add FFE for anat depending on the different echo numbers in dcm2bids.json

* Create a workflow to automate updating CHANGES.md (#562)

* Use text file to specify versions

* Add workflow to automate changelog

* Update CHANGES.md and version.txt for 1.1 release (#563)

* Update CHANGES.md and version.txt for 1.1 release

* Update the name of th esignal recovery PR

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Co-authored-by: po09i <47249340+po09i@users.noreply.github.com>
Co-authored-by: Alexandre D'Astous <po09i@hotmail.com>

* Update actions to more recent versions (#565)

* Compute phase and magnitude images from real/imaginary data (#551)

* Compute phase and magnitude in st_maths

* Add tests

* Fix tests and error messages

* Fix polarity to only be output in c... (continued)

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