PyDesigner v1.0-RC3

This version now optimally determines the best maximum spherical harmonic degree (l_max) for SH expansion. This will allow the expansion to always be well-conditioned despite the number of non-B0 single shells. This is implementation is based on https://mrtrix.readthedocs.io/en/dev/concepts/sh_basis_lmax.html.

fODFs computed by FBI fitting are now also saved as fbi_fodf.nii to allow FBI tractography. Please refer to MRtrix3's guide on using fODFs for tractography.

Added:

• FBI fODF map for FBI tractography. Users may use MRTrix3
  to further process this file.
• Variable maximum spherical harmonic degree to improve
  robustness of FBI fit. This was fixed at 6 previous, but has
  been defaulted to 6 now. Users may change l_max with the
  -l_max n flag. This is based on
  information found at https://mrtrix.readthedocs.io/en/dev/concepts/sh_basis_lmax.html

Changed:

• None

Removed:

• None

PyDesigner v1.0-RC2

Added:

• References to README.rst

Changed:

• The minimum B-value required for FBI (4000) is now inclusive
  instead of exclusive. This would allow executiong of FBI/FBWM
  for datasets with b=4000 mm/s^2
• Convert variable nthreads to string so subproces.run
  can recognize the flag
• Updated Slack permalink in README.rst

Removed:

• None

PyDesigner v1.0-RC1

This is a release candidate for a stable PyDesigner release. Despite most features being in their stable state, users are still encouraged to double check all extracted metrics. The notable features here are the addition of FBI and FBWM calculations.

Added:

• Methods to perform tensor only with compatible B-values. PyDesigner
  previously use all B-values in a DWI to do so. This behavior has
  been updated to use only B-values less than 2500
• FBI and FBWM calculations
• Brief documentation on how to run PyDesigner

Changed:

• Automatically issues dwipreproc or dwifslpreproc for
  compatibility with MRtrix3 >= 3.0.1
• Updated minimum version for required Python modules

Removed:

• None

PyDesigner v0.32

Added:

• Intrinsic inter-axonal and mean extra-axonal diffusivity
  calculation to WMTI

Changed:

• Method json2fslgrad converted from class method to function
  definition
• json2fslgrad now transposes B0s in BVAL file in accordance with
  FSL's gradient scheme
• Documentation update
• Extras directory renamed to extras
• DKE conversion scripts modified to correctly create ft and dke
  parameter files

Removed:

• None

PyDesigner v0.31

Added:

• NaN check in AWF calculculation that prevents further errors in intra-axonal
  and extra-axonal WMTI metrics computation

Changed:

• designer.fitting.dwipy input file detection method
• Dockerfile_release now deletes the correct temporary file to prevent build
  error

Removed:

• None

PyDesigner v0.3

Added:

• Head motion plot from on eddy_qc outputs
• Outlier plot from IRRLS outlier detection
• Updated documentation
• Option to reslice DWI with --reslice [x,y,z]

Changed:

• Flag --epiboost [index] changed to --rpe_pairs n, where
  users can specify the number of reverse phase encoded B0 pairs to
  use in EPI correction. Non-indexed B0s were previously destructively
  removed from DWI, leading to incorrect weighing of B0s in tensor
  estimation. The new method now preserves all B0s, thereby allowing
  faster EPI distortion correction without degrading DTI/DKI maps.
• Documentation moved to ReadTheDocs
• Moved B0 production module from designer.preprocessing.brainmask to
  a separate function at designer.preprocessing.extractmeanbzero()
  that gets called by PyDesigner main. This allows a B0.nii to be
  produced regardless of the --mask flag.

Removed:

• Documentation inconsistencies

The Cupid Release

With PyDesigner, users are no longer confined to specific file types, operating systems, or complicated scripts just to extract DTI or DKI parameters – PyDesigner makes this easy, and you will love it! You may download PyDesigner from GitHub, where you’ll find documentation [WIP] and a communication channel to get in touch with the devs. This is the first official release of PyDesigner ready for public use.

Key Features:
• 100% Python-based scripts
• Minimized package dependencies for small package footprint
• Preprocessing designed to boost SNR
• Accurate and fast DTI and DKI metrics via cutting-edge algorithms
• One-shot preprocessing to parameter extraction
• Cross-platform compatibility between Windows, Mac and Linux using Docker
• Highly flexible and easy to use
• Easy install with pip
• Input file-format agnostic – works with .nii, .nii.gz, .mif and dicoms
• Quality control metrics to evaluate data integrity – SNR graphs and outlier voxels
• Uses the latest techniques from DTI/DKI literature
• Boosts TOPUP speed with --epiboost flag for magnitudes faster EPI correction

Please direct all issues to the issues tab. Happy tensor imaging!

EDIT: Added fix for exception raised by --mask flag when running in a Docker environment

Bugfix update for 0.11-dev

dev-0.11

Dockerfile: disable removal of /tmp

0.1-dev: Merge pull request #87 from TheJaeger/docs/readme-update

This is the first developmental release of PyDesigner. Here's a list of what's included:

Preprocessing

1. Denoising
2. Degibbs
3. Eddy + EPI correction
4. Smoothing
5. Rician correction
6. Brain masking

Tensor Fitting

1. IRWLLS outlier detection
2. WLLS fitting
3. AKC outlier detection
4. DTI/DKI parameter extraction

Report issues in issues tab. We will update milestones for 0.2-dev release based on feedback from this release's testing.