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Change Log

All notable changes to AMICO will be documented in this file.

v2.0.3
2024-07-04

🐛Fixed

  • Wrong diffusivity value in the set() method of the NODDI model (typo introduced in f070c23)

v2.0.2
2024-07-04

✨Added

  • Added cp312 wheels to github actions

🛠️Changed

  • Restict the numpy version to <2.0.0 (due to dipy problems)
  • Parameters in the set() method of the models have now default values
  • MacOS arm64 wheels are now compiled with GitHub Actions instead of Cirrus CI

🐛Fixed

  • Link to installation guide in README.md
  • Improved print() statements when running from Jupyter notebooks

v2.0.1
2023-09-21

🛠️Changed

  • Bump dmri-dicelib to v1.0.1

🐛Fixed

  • Implement the set() method in the VolumeFractions model

v2.0.0
2023-09-14

🛠️Changed

  • From multiprocessing to multithreading (huge speedup in models fit! 🚀)
    • models and lut modules in Cython
    • fit() methods in Cython
    • dir_to_lut_idx() method in Cython
  • New NODDI maps names:
    • from ICVF to NDI
    • from OD to ODI
    • from FISO to FWF
  • New output images name casing (e.g. from FIT_NDI.nii.gz to fit_NDI.nii.gz)
  • Default Diffusion Tensor model fit method to compute the primary direction in each voxel from WLS to OLS
  • Default number of threads used by BLAS libraries from -1 (all threads) to 1
  • Parallel threads config name from parallel_jobs to n_threads
  • Default study_path='.' and subject='.' in core.Evaluation()
  • Default ndirs=500 in core.generate_kernels()
  • Expire the deprecated ndirs parameter in core.setup()
  • Replace tqdm with dicelib.ui.ProgressBar()
  • Switched to proprietary license (see LICENSE file)

✨Added

  • C++ interfaces for NNLS and LASSO solvers (provided by spams-cython)
  • DTI_fit_method config to choose the Diffusion Tensor model fit method (from DIPY)
    • OLS (Ordinary Least Squares)
    • WLS (Weighted Least Squares)
  • BLAS_n_threads config to set the number of threads used in the threadpool-backend of common BLAS implementations (e.g. OpenBLAS)
  • doComputeRMSE config to compute the Root Mean Square Error image
  • doSaveModulatedMaps to compute modulated maps for the NODDI model (Tissue-weighted mean), e.g. fit_NDI_modulated.nii.gz

🐛Fixed

  • DeprecationWarning: dipy.reconst.shm.real_sym_sh_basis (with dipy>=1.4.0)

[1.5.4] - 2023-02-15

Fixed

  • invalid command 'bdist_wheel' error when install with pip <= v20.0.2
  • #155 Replaced the NiBabel get_data() method with get_fdata() (raise ExpiredDeprecationError with NiBabel >= v5.0.0)

[1.5.3] - 2023-01-23

Fixed

  • Problem with the set_solver() method that raise a multiple values for keyword argument error
  • Replaced np.bool, np.float and np.object deprecated aliases (raise AttributeError with NumPy >= v1.24.0)

[1.5.2] - 2022-10-21

Added

  • 'b0_min_signal' parameter in 'load_data()' to crop to zero the signal in voxels where the b0 <= b0_min_signal * mean(b0[b0 > 0])
  • 'replace_bad_voxels' parameter in 'load_data()' to replace NaN and Inf values in the signal

[1.5.1] - 2022-09-21

Fixed

  • Check if DWI file is a 4D image
  • Removed unused 'verbose' option in init (now all is controleld by 'set_verbose')

[1.5.0] - 2022-07-06

Changed

  • Implemented the 'synthesis.py' module for kernels generation
  • 'datasynth' tool (CAMINO) no more needed

[1.4.4] - 2022-06-14

Fixed

  • Import error in 'util.py' on Windows systems
  • Loading errors in 'lut.py' on Windows systems

[1.4.3] - 2022-05-18

Fixed

  • Problems with joblib and pickle on some systems (issue #136)
  • Added 'packaging' to requirements as it is not present by default on some systems

Changed

  • Removed config option 'parallel_backend' as only 'loky' works in current implementation

[1.4.2] - 2022-03-26

Fixed

  • Bug when using 'doSaveCorrectedDWI' (issue #134)

[1.4.1] - 2022-03-20

Fixed

  • Replace all 'print' with 'PRINT'

[1.4.0] - 2022-03-04

Added

  • Function 'amico.set_verbose' to control what is printed during execution

Changed

  • Required dependency from 'python-spams' to 'spams'

[1.3.2] - 2022-01-31

Changed

  • Required dependency numpy>=1.12,<1.22
  • amico.core.setup: removed 'ndirs' parameter, now precomputes all directions

Added

  • Shortcut 'amico.core.setup' to 'amico.setup'

[1.3.1] - 2021-12-03

Fixed

  • Removed unused hasISO parameter in experimental VolumeFractions model

Changed

  • Install information are stored (and taken from) amico/info.py

[1.3.0] - 2021-10-27

Added

  • Possibility to fit different voxels in parallel
  • Config options 'parallel_jobs' and 'parallel_backend' for better control of parallel execution
  • Possibility to specify d_perp<>0 for the Stick in StickZeppelinBall

Fixed

  • Forcing SPAMS to use only one thread
  • Added missing dependencies, e.g. wheel

Changed

  • Replaced in-house progress bar to tqdm

[1.2.10] - 2021-05-20

Fixed

  • Warning message in util.py fsl2scheme and sandi2scheme

[1.2.9] - 2021-02-23

Added

  • Controls if files exist before opening

Fixed

  • Wrong datatype when saving results

[1.2.8] - 2021-01-29

Added

  • SANDI model

[1.2.7] - 2020-10-28

Added

  • Possibility to set one single direction in the LUT resolution

[1.2.6] - 2020-10-22

Added

  • Function get_params to get the specific parameter values of a model

[1.2.5] - 2020-08-06

Changed

  • Moved the documentation to the Wiki

[1.2.4] - 2020-06-10

Added

  • Added the parameter 'd_par_zep' in the StickZeppelinBall model

[1.2.3] - 2020-05-25

Fixed

  • Modify setup.py and fix spams dependency

[1.2.2] - 2020-05-05

Fixed

  • Checks if input mask is 3D.

[1.2.1] - 2020-04-25

Changed

  • Use d_perps to set models instead of ICVFs.
  • Canged case of some parameters for consistency

[1.2.0] - 2020-04-01

Added

  • Functions to colorize the output messages.

[1.1.0] - 2019-10-30

This version of AMICO is not compatible with COMMIT v1.2 of below. If you update AMICO to this version, please update COMMIT to version 1.3 or above.

Added

  • Changelog file to keep tracking of the AMICO versions.
  • New feature that allows to decrease the LUT resolution. Example here.