Releases | Open Source Science

rapidtide - Version 3.0.11 - 8/27/25 Urgent container fix

(Docker) Fixed a critical bug in building the container.
(happy) Added the ability to specify an overall processing mask.
(docs) Revised the singularity/apptainer installation section.
(reference) Added MNI152NLin2009cAsym versions of the JHU atlases.
(package) Miscellaneous code cleanups.
(package) More dependabot PRs.

- Python
Published by bbfrederick 6 months ago

rapidtide - Version 3.0.10 - 8/18/25 checkpoint release

(tidepool) Do better checking on which required files exist so it's more clear why a dataset won't load.
(tidepool) Add support for PySide6 (in addition to PyQt5 and PyQt6).
(docs) Clarified that the sLFO filtered output of rapidtide has NO other filtering applied to is - the temporal, spatial, and confound filtering is all discarded prior to the final sLFO filtering step.
(package) Played with some coding models (qwen3-coder, Claude) to write some docstrings and check a few routines for bugs. It generally worked well, but you definitely have to check their work.
(package) Adjusted coverage calculation.
(package) Added a test for data simulation.
(package) Accepted several dependabot PRs.

- Python
Published by bbfrederick 7 months ago

rapidtide - Version 3.0.9 - 7/3/25 Add classic RIPTiDe, internal code reorganization

(rapidtide) Added an alternative method for coarse delay estimation (set --similaritymetric riptide to select). This uses a fit to a set of delayed regressors (actually, this is the original RIPTiDe method from ~2010).
(rapidtide) Separated coarse delay estimation and similarity function fitting into two separate workflows (they were together in v3.0.8).
(rapidtide) Fixed a stupid bug in the placement of the delay refinement code block for each pass.
(rapidtide) Laid most of the groundwork for dynamically switching delay estimation methods and parameters between passes.
(package) Accepted several dependabot PRs.

- Python
Published by bbfrederick 8 months ago

rapidtide - Version 3.0.8 - 6/26/25 A bugfix, and massive, hopefully invisible, internal changes

(rapidtide) Fix https://github.com/bbfrederick/rapidtide/issues/213 (thanks to https://github.com/tomosumi for reporting the bug).
(rapidtide) Split coarse delay estimation and fitting out into a separate workflow.
(rapidtide) Split delay refinement out into a separate workflow.
(rapidtide) Split regressor refinement out into a separate workflow.
(rapidtide) All this is in preparation for a new, modular workflow with more flexible control of the fitting process. It's not done yet, butthis is getting all internal code blocks ready for it. I want to pause here to make sure I haven't broken anything (all the automated tests pass, but I want to be careful).
(docs) Some improvement to the tidepool section.
(package) Made a more streamlined and rational interface for allocating shared memory.
(package) Resolved incompatibility of statsmodels and scipy>1.15.3.
(package) Accepted several dependabot PRs.

- Python
Published by bbfrederick 8 months ago

rapidtide - Version 3.0.7.1 - 6/16/25 Quick patch to v3.0.7

(rapidtide) Disabled sLFO filtering by default. Use sLFOfiltmask to turn it on.
(retroregress) Synced with sLFO filtering changes to rapidtide.

- Python
Published by bbfrederick 9 months ago

rapidtide - Version 3.0.7 - 6/16/25 happy speedup and other QOL improvements

(rapidtide) Save the full autocorrelation function of the probe regressor at each pass.
(rapidtide) Now save a version of the mean fMRI image prior to filtering
(rapidtide) Added the abilty to disable masking of sLFO filter. Use --nosLFOfiltmask to disable.
(happy) Implemented multiprocessing for detrending, phase projection, and phase projection smoothing.
(happy) Precache convolution gridding kernel outputs to improve repeatability.
(happy) Early implementation of Wright's method for finding vessels.
(showarbcorr) Fixed some internal issues.
(simdata) Many changes to finetune the simulation and make the output more realistic. Still in progress.
(Docker) Turned on provenance and sbom in Docker builds.
(package) Accepted several dependabot PRs.

- Python
Published by bbfrederick 9 months ago

rapidtide - Version 3.0.6 - 5/21/25 Updated internal multiprocessing code

(rapidtide) Made a generic, reusable multiprocessing module and moved many functions over to it.
(ccorrica) Samplerate is now set properly if input is a BIDS tsv file.
(package) Added several new tests.

- Python
Published by bbfrederick 10 months ago

rapidtide - Version 3.0.5 - 5/7/25 small bug fix

(rapidtide) Loosened the sample rate matching when appending timecourses to files, and read NIFTI tr values using modern header features. This should help address https://github.com/bbfrederick/rapidtide/issues/205 (thank you to https://github.com/phildeming for finding this).

- Python
Published by bbfrederick 10 months ago

rapidtide - Version 3.0.4 - 5/5/25 Versions! And bug fixes.

(rapidtide, retrotregress, tidepool) Support for maxcorrrefined map.
(retroregress) Gracefully handles missing mask names in runoptions file.
(package) Version works again! Thank you Chris (https://github.com/effigies)!
(package) Added a few more tests to catch edge cases that showed up in testing fmripost-rapidtide.

- Python
Published by bbfrederick 10 months ago

rapidtide - Version 3.0.3 - 5/4/25 Stability increases and regional timecourses

(rapidtide, retroregress) If you supply a brain, GM, WM, or CSF mask, rapidtide extracts the matching timecourse from the mask at startup, and after filtering, if it's done. retroregress extracts the timecourses after filtering.
(rapidtide) Fixed mask logic when gray matter mask is provided.
(rapidtide) Fixed a crash when --acfix is selected and a bad sidelobe is encountered if the similarity calculation range is not the entire timecourse (THAT was hard to pin down...).
(rapidtide, tidepool) Fixed a serious cosmetic bug in corrout files introduced in v3.0.2 - teoffset was not being set properly by rapidtide, so the tidepool similarity function display was very wrong.
(rapidtide) shiftedtcs file is now written during each pass if --saveintermediatemaps is set and --outputlevel is more or max (in response to a feature request).
(rapidtide) Added back the ability to have integral powers of the motion regressors.
(rapidtide) Added the ability to specify a CSF mask.

- Python
Published by bbfrederick 10 months ago

rapidtide - Version 3.0.2 - 4/28/25 retroregress upgrade

(retroregress) Added a new argument to --outputlevel, onlyregressors. When selected, retroregress generates the voxel specific sLFO regressor(s), saves them, and exits. This option exists so that you can use the rapidtide voxel specific sLFO regressors in an external processing routine such as XCP-D without extraneous data storage or processing time.
(rapidtide) Leaned harder into using the voxelData class, and beefed up its capabilities.
(happy) Updated to use voxelData.
(happy) Moved phase projection to an external routine.
(documentation) Fixed a few more typos.

- Python
Published by bbfrederick 10 months ago

rapidtide - Version 3.0.1 - 4/23/25 Documentation fix

(documentation) I missed a bunch of weird errors in the "Theory of Operation" section. Are you surprised? I'm not surprised. You shouldn't be either. These are now fixed. This doesn't change any code - mostly affects online documentation.

- Python
Published by bbfrederick 11 months ago

rapidtide - Version 3.0 - 4/22/25 New version release!

(documentation) Added summary of 3.0 changes, fixed a few typos.

- Python
Published by bbfrederick 11 months ago

rapidtide - Version 3.0alpha15 - 4/22/25 Final cleanup before release

(rapidtide) Fixed a bug in masking logic introduced in last version.
(rapidtide) Pullled regressor cleaning steps out into a separate routine.
(rapidtide) Removed unused "noiseregressor" code. Its functionality is now covered with confound regression.
(rapidtide) Removed memory profiling code that relied on an unsupported library.
(rapidtide) Defined a new class to handle the input data. This simplifies a lot of internal operations.
(happy) Updated deep learning filter training and inference code, and saved models, for better tensorflow 2 compatibility.
(docs) Updated installation instructions.
(package) Updated copyright notices.

- Python
Published by bbfrederick 11 months ago

rapidtide - Version 3.0alpha14 - 4/8/25 preRC prerelease

(rapidtide) Rationalized handling of zero-mean data - now use the --dataiszeromean argument to tell rapidtide how to make masks. --globalmaskmethod no longer exists.
(retroregress) Some bugfixes.
(atlasaverage) 4D file timecourse output is now a BIDS compliant json/tsv.gz pair, with timecourse labels, if desired.
(delayvar) Secret bugfixes.
(package) Fixed definition of APARC_WHITE to add cerebral white matter (oops!).
(package) Made it easier to run local tests.
(docs) Expanded theory of operation section.

- Python
Published by bbfrederick 11 months ago

rapidtide - ## Version 3.0alpha13 - 3/31/27 Bugs and features

(rapidtide, retroglm) Preserve the sign of the GLM fit R value (it might be useful for distinguishing arterial blood).
(rapidtide) Fixed a bug with --dofinalrefine - now the shiftedtcs file IS written.
(delayvar) New secret program, for secret purposes, to satisfy a secret question I had. More later.
(package) Clarified that the final sLFO removal filter does NOT use a GLM (the current filter is an OLS filter).

- Python
Published by bbfrederick 11 months ago

rapidtide - Version 3.0alpha12 - 3/19/25

(rapidtide) Added option to perform regressor refinement on last pass.
(rapidtide) Moved regressor refinement out into its own class to make things more modular.
(refinedelay) Put in some experimental code to do multiderivative delay fits. Currently doesn't work very well.
(tidepool) Changed default colormaps for similarity width, MTT.
(package) Made a script to compile qt templates.
(package) Added the ability to set value limits to some parser functions.

- Python
Published by bbfrederick 12 months ago

rapidtide - ## Version 3.0alpha11 - 3/5/25 tidepool enhancements

(tidepool) Substantial speed improvement switching datasets.
(tidepool) Colormap radio button is now set correctly.
(tidepool) Mask menu label is now set correctly when restoring a loaded dataset.
(versioneer) Updated to 0.29.
(docs) tidepool's documentation has been updated to reflect the current state of the program.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha10 - 2/28/25 More tidepool enhancements

(tidepool) Full support for multiple concurrent datasets. Dataset loading and selection is now done through the File menu.
(tidepool) Load additional informational maps, and somewhat more intelligently.
(tidepool) Fixed pane loading to use all available panes.
(tidepool) Fixed image saving under pyqt6.
(tidepool) For the regressor spectrum, only do FFT of the portion of the regressor used for similarity calculation.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha9 - 2/26/25 Tidepool enhancements

(rapidtide) Fixed the calculation of the regressor autocorrelation width (used in estimating MTT).
(tidepool) First working version that allows loading multiple files. Use --dataset DATASET1 DATASET2....
(tidepool) Added new "big" template to let you see more information at once. Select with --uistyle big.
(tidepool) Pretty significant code cleanup under the hood.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha8 - 2/20/25 Bugfix

(rapidtide) Enhanced fit failure reporting.
(rapidtide) Fixed map output type for non-float maps.
(tidepool) Clarify how you specify the dataset name in the help text.
(tidepool) Fixed some typos in outputs.
(tidepool) Made some internal changes in preparation for allowing loading multiple files.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha7 - 2/11/25

(happy) Trying out some new approaches for aliased correlation.
(happy) Put in some initial support for multiecho data.
(happy) Updated argument parser, adjusted some argument names.
(package) Various modernizations and cleanups.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha6 - 1/28/25 happy bugfix

(happy) Fixed a major bug in motion filtering (thank you to Sukru Demiral for reporting it!)

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha5 - 1/25/25

(happy) Fixed a typo in argument description.
(atlasaverage) Added the ability to segment a template atlas based on values of the map being summarized.
(docs) Significantly beefed up happy section.
(reference) Constructed a new version of the JHU LVL1 atlas where each territory is split into an early and late subterritory, based on the median delay in the HCP-YA dataset.
(package) Fully converted to using pyproject.toml for packaging.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha4 - 1/21/25 bug fix, significance mask enhancement

(rapidtide, tidepool) Both now only use neglog10p map to dynamically make significance masks.
(rapidtide, Docker) rapidtide should now properly report it's version number in a container even if it is in prerelease.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha3 - 1/16/25

(rapidtide) Refine delay is now on by default. Use --norefinedelay to disable it. --refinedelay still exists for compatibility, but does nothing.
(rapidtide) Now outputs a map of fit significance (-log10(p)). In response to https://github.com/bbfrederick/rapidtide/issues/174.
(showxcorrx) Fixed some issues with axis labelling.

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha2 - 12/30/24 Critical bug fix and an enhancement

(happy, rapidtide) Now do (correct) checking to see if running in a container that now handles both Docker and Singularity/Apptainer properly. Thank you to Derek Monroe (https://github.com/dcmonroe) for the catch and the fix!
(package) Now includes codespell checking thanks to Yaroslav O. Halchenko (https://github.com/yarikoptic)!

- Python
Published by bbfrederick about 1 year ago

rapidtide - Version 3.0alpha1 - 12/20/24 First alpha of rapidtide 3.0

(rapidtide) The --fixdelay option has been split into two options. --initialdelay DELAY lets you specify either a float that sets the starting delay for every voxel to that value, or a 3D file specifying the initial delay for each voxel. --nodelayfit determines whether the delay can be adjusted from its initial value. Closes https://github.com/bbfrederick/rapidtide/issues/171. KNOWN ISSUE: If you supply an initial delay map, instead of using the global mean, you should use the delays to make your first stage regressor. Currently that is not the case.
(rapidtide) Reorganized command line options and adjusted the default values.
(rapidtide) Help output now shows the filter ranges.
(rapidtide, retroglm) Added delay refinement using the ratio of the fit coefficients of the regressor and its time derivative.
(rapidtide, retroglm) Fixed a bad shared memory leak.
(retroglm) Significantly enhanced logging.
(retroglm) Added canary files.
(rapidtide) Implemented delay map patching.
(rapidtide) Write out individual EV timecourses.
(Docker) Cleaned up some internal variables.
(Docker) Improved build and testing scripts.
(io) Added function to compare nifti files with some tolerance.
(docs) Automated more table generation.
(package) Merged some dependabot PRs.
(package) Fixed a fairly big, but not necessarily impactful bug. mlregress returned R2, not R, so anything referring to the R of a fit was actually squared (R was actually R2, R2 was actually R4).

- Python
Published by bbfrederick about 1 year ago