From a67853f3b1cee60b17df8083b84a6ad1e409f1f1 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 21 Nov 2023 08:00:30 -0500 Subject: [PATCH] DOC: Expand release notes --- CHANGES.rst | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/CHANGES.rst b/CHANGES.rst index b2f264965..0dbaeb742 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -11,11 +11,11 @@ as previous versions. ``minimal`` will produce only the minimum necessary to deterministically generate the remaining derivatives. ``resampling`` will produce some additional derivatives, intended to simplify resampling with other tools. -The ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``. -If provided, fMRIPrep will read the specified directories for pre-computed -derivatives. If a derivative is found, it will be used instead of computing -it from scratch. If a derivative is not found, fMRIPrep will compute it and -proceed as usual. +The ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``, +for example ``--derivatives anat=$SMRIPREP_DIR``. If provided, fMRIPrep will +read the specified directories for pre-computed derivatives. If a derivative is +found, it will be used instead of computing it from scratch. If a derivative is +not found, fMRIPrep will compute it and proceed as usual. Taken together, these features can allow a dataset provider to run a minimal fMRIPrep run, targeting many output spaces, while a user can then run a @@ -24,9 +24,16 @@ spaces they need. Another use case is to provide an precomputed derivative to override the default fMRIPrep behavior, enabling easier workarounds for bugs or experimentation with alternatives. -Additionally, this release includes a number of bug fixes and minor improvements. -In particular, susceptibility distortion correction has been improved for -PEPolar, phase difference and direct fieldmaps. +Additionally, this release includes a number of bug fixes and improvements. +This release adds support for MSM-Sulc, improving the alignment of subject +surfaces to the fsLR template. This process is enabled by default, but may +be disabled with the ``--no-msm`` flag. + +This release resolves a number of issues with fieldmaps inducing distortions +during correction. Phase difference and direct fieldmaps are now masked correctly, +preventing the overestimation of distortions outside the brain. Additionally, +we now implement Jacobian weighting during unwarping, which corrects for compression +and expansion effects on signal intensity. Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric