Rapidtide

Latest version: v2.9.9.5

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2.2.7.1

Not secure
* (Dockerfile) Updated to a consistent python environment.

2.2.7

Not secure
* (rapidtide) Fixed GLM noise removal in CIFTI files.
* (rapidtide) Initial support for linear rather than circular correlation.
* (happy) Fixed some pretty broken masking logic when you want to process more (rather than less) voxels than the brain.

2.2.6

Not secure
* (fingerprint) Various fixes to mask handling.
* (package) Staged some prep work on updating the setup/installation files.

2.2.5

Not secure
* (rapidtide) Postprocess timing information to make it more useful.
* (rapidtide) Re-enabled numba by default.
* (fingerprint) Fixed handling of 4D atlases, empty regions, and 4D masks. Added "constant" template, and allow 0th order processing (mean).
* (atlastood) Fixed 4D atlas handling. Now mask atlas after collapsing to 3D.
* (histnifti) Added ``--transform`` flag to map values to percentiles.

2.2.4

Not secure
* (fingerprint) Now works properly for 3D input files.
* (tidepool) Turned the default level of verbosity way down, but gave you the ability to crank it back up.
* (RapidtideDataset.py) Fixed the default type of "numberofpasses".

2.2.3

Not secure
* (rapidtide) Added a new feature, ``--globalmeanselect``, to try to locate a good, uniform, short delay pool of voxels to use for the initial global mean signal. This is an attempt to fix the "poison regressor" problem - if the initial regressor contains data from multiple, distinct pools of voxels with different delays, the initial global regressor is strongly autocorrelated, and delay fits become ambiguous. This cannot be corrected by refinement, so better to avoid it altogether. This option selects only voxels with clear, short delays, after a single pass with despeckling disabled. The result is a mask (XXXdesc-globalmeanpreselect_mask.nii.gz) that can be used with ``--globalmeanincludemask`` for a subsequent run.
* (rapidtide) Fixed a nasty bug that caused offsettime and lagminthresh to interact incorrectly, sometimes leading to almost no voxels for refinement.
* (happy) Moved some code around, changed some internal names, and added secret bits to support future, secret, features.
* (tidepool) Trying to add a little more clarity to the user about image orientation (the image's affine transform is correct, so the mapping between voxel and MNI coordinate is correct, but currently it's not clear if displayed images are radiological or neurological orientation.
* (fingerprint) Added the JHU atlases as options.
* (package) Added slightly modified version of the JHU arterial territorial atlases to the reference section (Paper: https://doi.org/10.1101/2021.05.03.442478, Download: https://www.nitrc.org/projects/arterialatlas).
* (Docker) Fixed a dependency problem for pyfftw (resolves https://github.com/bbfrederick/rapidtide/issues/79)
* (pony) One time offer, today only - every user gets a pony upon request!

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