Merge branch 'master' of https://github.com/muscbridge/PyDesigner

298 Update PyDesigner for Official v1.0.0 Release (#299)

* Update license information

* Update gitignore to avoid builds

* Update documentation

* Update Dockerfiles for latest FSL installer

* Remove AKC from standard processing

* Update docs

Fix logic in multi-TE protocol detection (#283)

* Update logic to handle multi-TE

* Update docs

* Update .gitignore

* Update docs

* Remove requirement to separate inputs paths with comma

* Update version to v1.0-RC12

* Update CHANGELOG

Fix for SciPy cmake error (#272)

Fix HDF5 issues in Docker build (#258)

* Add `echotime` function

* Add TE awareness to DWIParser

* Add `dwiextract` function

Extracts DWI volumes from star:end index

* Add filename dictionary

* Adjust tensor type thresholds

* Add maxFBIBval() method

* Fine tune tensor type thresolhds

* Add fit regime function

Eases full automation of pipeline

* Fix #232 by mitigating large values

* Incorporate fit regime into main

* Fix #255 by introducing overflow mitigation

* Introduce proper indexing of b-value shells in FBI/FBWM

* Add more proper handling of b-value shells

* Add multi-TE support to main

* Minor documentation changes

* Disable B0 exclusion in IRLLS

* Update version to RC10

* Update filenaming algorithm

* Add doc files

* Update CHANGELOG

* Remove unused print statement

* Add `--no_rectify` flag

* Update CHANGELOG

* Update documentation

* Remove unused doc files

* Update PyDesigner Logo

* Update Sphinx documentation

* Update Dockerfiles to include HDF5

Fix b-value rounding to integer (#251)

* Fix max shell int rounding

* Update documentation

Fix type in MANIFEST (#250)

Docker build fixes (#247)

Fixes errors arising in PyDesigner installation due to CMake

Update shell-sampling determination (#241)

* Fix DTI protocol (#228)

* Update reslicing to use new `mrgrid` command

This also works with older `mrreslice`

* Fix bad indent in tensorReorder()

* Update documentation

* Add bval scaling (#230)

* Fix SNR plotting issues (#233)

* Add try/except loop to SNR plot

* Fix eddy path when `--noqc` is parsef

* Fix a bad indent

* Update CHANGELOG

* Init tractography module (#234)

* Init tractography module with DSI Studio

* Update main to use tractography modules

* Update version and MANIFEST

* Update docs

* Fiber Tracking: FBI tractography (#235) (#237)

* Fix DTI protocol (#228)

* Update reslicing to use new `mrgrid` command

This also works with older `mrreslice`

* Fix bad indent in tensorReorder()

* Update documentation

* Add bval scaling (#230)

* Fix SNR plotting issues (#233)

* Add try/except loop to SNR plot

* Fix eddy path when `--noqc` is parsef

* Fix a bad indent

* Update CHANGELOG

* Init tractography module (#234)

* Init tractography module with DSI Studio

* Update main to use tractography modules

* Update version and MANIFEST

* Update docs

* Change dki_ak fname (#238)

* Update shell sampling determination (#240)

* Add new functions to determine DWI shell sampling

* Remove references to old functions

* Change how shell sampling is determined

* Update documentation

Bugfix for dki_ak not being saved (#239)

* Fix DTI protocol (#228)

* Update reslicing to use new `mrgrid` command

This also works with older `mrreslice`

* Fix bad indent in tensorReorder()

* Update documentation

* Add bval scaling (#230)

* Fix SNR plotting issues (#233)

* Add try/except loop to SNR plot

* Fix eddy path when `--noqc` is parsef

* Fix a bad indent

* Update CHANGELOG

* Init tractography module (#234)

* Init tractography module with DSI Studio

* Update main to use tractography modules

* Update version and MANIFEST

* Update docs

* Fiber Tracking: FBI tractography (#235) (#237)

* Fix DTI protocol (#228)

* Update reslicing to use new `mrgrid` command

This also works with older `mrreslice`

* Fix bad indent in tensorReorder()

* Update documentation

* Add bval scaling (#230)

* Fix SNR plotting issues (#233)

* Add try/except loop to SNR plot

* Fix eddy path when `--noqc` is parsef

* Fix a bad indent

* Update CHANGELOG

* Init tractography module (#234)

* Init tractography module with DSI Studio

* Update main to use tractography modules

* Update version and MANIFEST

* Update docs

* Change dki_ak fname (#238)