# What's New

## 1.1.1

This release fixes a major bug in QSIRecon's handling of multi-session and multi-run datasets.
When processing multiple sessions or runs in a single QSIRecon call, the reconstruction workflow was being modified in place,
such that the first session/run was processed correctly, but subsequent sessions/runs were processed with global default values.
This bug primarily affected custom reconstruction workflows.
The built-in workflows should be largely unaffected.

### 🎉 Exciting New Features

* Parcellate scalars and write out brain mask by @tsalo in https://github.com/PennLINC/qsirecon/pull/251
* Use deltas in DIPY interfaces by @tsalo in https://github.com/PennLINC/qsirecon/pull/259

### 🐛 Bug Fixes

* Upgrade DIPY, pyAFQ by @36000 in https://github.com/PennLINC/qsirecon/pull/235
* Fix handling of atlas labels with spaces and test custom atlas handling by @tsalo in https://github.com/PennLINC/qsirecon/pull/248
* Remove background label from atlases before calculating connectivity by @tsalo in https://github.com/PennLINC/qsirecon/pull/249
* Fix collection of longitudinal anatomical outputs by @tsalo in https://github.com/PennLINC/qsirecon/pull/253
* Write out ACPC-space scalars from TORTOISE node if estimate_mapmri is False by @tsalo in https://github.com/PennLINC/qsirecon/pull/254
* Prevent workflow spec dictionary from being modified in place during build process by @tsalo in https://github.com/PennLINC/qsirecon/pull/263

### Other Changes

* Update boilerplate.bib for mrtrix reference by @chiuhoward in https://github.com/PennLINC/qsirecon/pull/239
* Update descriptions of scalar map parameters by @tsalo in https://github.com/PennLINC/qsirecon/pull/225
* Generate figure showing scalar maps by @tsalo in https://github.com/PennLINC/qsirecon/pull/246
* Remove outdated admonition by @tsalo in https://github.com/PennLINC/qsirecon/pull/257
* Add missing workflows to "which workflows are appropriate" table by @tsalo in https://github.com/PennLINC/qsirecon/pull/258
* Fix table borders by @tsalo in https://github.com/PennLINC/qsirecon/pull/260
* Add unused `plot_reports` input to `_KurtosisReconstructionInputSpec` by @tsalo in https://github.com/PennLINC/qsirecon/pull/262

## New Contributors
* @36000 made their first contribution in https://github.com/PennLINC/qsirecon/pull/235

**Full Changelog**: https://github.com/PennLINC/qsirecon/compare/1.1.0...1.1.1


## 1.1.0

### 🎉 Exciting New Features

* Tissue fraction modulated ICVF and OD maps by @araikes in https://github.com/PennLINC/qsirecon/pull/218
* Calculate kurtosis microstructure scalars with new `DKI_reconstruction` parameter by @tsalo in https://github.com/PennLINC/qsirecon/pull/223

### Other Changes

* Add `smoothing` and `otsu_threshold` autotrack arguments by @smeisler in https://github.com/PennLINC/qsirecon/pull/219
* Allow desc entity in recon scalar derivatives by @tsalo in https://github.com/PennLINC/qsirecon/pull/220

## New Contributors

* @araikes made their first contribution in https://github.com/PennLINC/qsirecon/pull/218

**Full Changelog**: https://github.com/PennLINC/qsirecon/compare/1.0.1...1.1.0

## 1.0.1

### 🎉 Exciting New Features

* Add DSIQ5 extrapolation option by @tsalo in https://github.com/PennLINC/qsirecon/pull/214

### 🐛 Bug Fixes

* Clip negative values in extrapolation interfaces by @tsalo in https://github.com/PennLINC/qsirecon/pull/213

### Other Changes

* Fixes small docs typo: "scelar" => "scalar" by @arokem in https://github.com/PennLINC/qsirecon/pull/203
* Fix FA description in DSIStudio outputs by @smeisler in https://github.com/PennLINC/qsirecon/pull/198

### New Contributors

* @arokem made their first contribution in https://github.com/PennLINC/qsirecon/pull/203

**Full Changelog**: https://github.com/PennLINC/qsirecon/compare/1.0.0...1.0.1

## 1.0.0

### 🛠 Breaking Changes

* Rename QSIPrep to QSIRecon by @tsalo in https://github.com/PennLINC/qsirecon/pull/1
* Start removing QSIPrep-specific code and documentation by @tsalo in https://github.com/PennLINC/qsirecon/pull/4
* Remove QSIPrep-specific parameters and Config elements by @tsalo in https://github.com/PennLINC/qsirecon/pull/6
* Drop Docker wrapper by @tsalo in https://github.com/PennLINC/qsirecon/pull/52
* Restructure outputs into BIDS datasets by @tsalo in https://github.com/PennLINC/qsirecon/pull/66
* Combine `mfp` and `mdp` entities into single `param` entity by @tsalo in https://github.com/PennLINC/qsirecon/pull/72
* Replace `--recon-input-pipeline` with `--input-type` by @tsalo in https://github.com/PennLINC/qsirecon/pull/68
* Remove unused `--longitudinal` argument by @tsalo in https://github.com/PennLINC/qsirecon/pull/88
* Make all params and models lower-case by @tsalo in https://github.com/PennLINC/qsirecon/pull/90
* Reorganize atlas management based on XCP-D and BIDS-Atlas by @tsalo in https://github.com/PennLINC/qsirecon/pull/123
* Rename `--freesurfer-input` to `--fs-subjects-dir` by @tsalo in https://github.com/PennLINC/qsirecon/pull/152
* [ENH] Read session-specific anat data by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/151
* Remove underscore versions of all parameters by @tsalo in https://github.com/PennLINC/qsirecon/pull/159
* Make connectivity field names compatible with MATLAB by @tsalo in https://github.com/PennLINC/qsirecon/pull/166

### 🎉 Exciting New Features

* Add ng, perng, parng, and mapcoeffs to Dipy MAPMRI outputs by @tsalo in https://github.com/PennLINC/qsirecon/pull/55
* Add DatasetLinks to dataset_description.json by @tsalo in https://github.com/PennLINC/qsirecon/pull/77
* Pass DWI file metadata to reconstruction workflows by @tsalo in https://github.com/PennLINC/qsirecon/pull/154
* Add HBCD Release1 recon workflow by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/169

### 🐛 Bug Fixes

* Write out QSIRecon pipeline-wise reports by @tsalo in https://github.com/PennLINC/qsirecon/pull/7
* Write out reports to individual reconstruction derivative folders by @tsalo in https://github.com/PennLINC/qsirecon/pull/53
* Add summary reportlets to HTML report by @tsalo in https://github.com/PennLINC/qsirecon/pull/61
* Fix QSIRecon Entrypoint by @smeisler in https://github.com/PennLINC/qsirecon/pull/76
* Use file lock to avoid concurrent edits to dataset_description.json by @cookpa in https://github.com/PennLINC/qsirecon/pull/91
* Compress the tck files by @tsalo in https://github.com/PennLINC/qsirecon/pull/93
* Add missing filename patterns by @tsalo in https://github.com/PennLINC/qsirecon/pull/131
* Fix infant anatomical ingression by @tsalo in https://github.com/PennLINC/qsirecon/pull/126
* Fix extension in ds_fs_5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/165
* Fix extension in ds_qsiprep_5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/172
* Fix space in ds_qsiprep_5tt_hsvs by @tsalo in https://github.com/PennLINC/qsirecon/pull/175
* Make PlotPeaks robust enough that we don't need --writable-tempfs in singularity/apptainer by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/174

### Other Changes

* Remove internal version of LiterateWorkflow by @tsalo in https://github.com/PennLINC/qsirecon/pull/8
* Drop and modify infrastructure files by @tsalo in https://github.com/PennLINC/qsirecon/pull/40
* Remove QSIPrep-specific tests by @tsalo in https://github.com/PennLINC/qsirecon/pull/5
* Drop unused modules, classes, and functions by @tsalo in https://github.com/PennLINC/qsirecon/pull/11
* [CI] Speed up pyafq test by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/57
* [DOCS] Reorganize documentation by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/56
* Collect templates from TemplateFlow instead of package data by @tsalo in https://github.com/PennLINC/qsirecon/pull/49
* Remove unused data files by @tsalo in https://github.com/PennLINC/qsirecon/pull/63
* Replace hyperlinks with BibTeX references by @tsalo in https://github.com/PennLINC/qsirecon/pull/67
* [DOCS] Add scalar tables by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/80
* Move scalar file configs to YAMLs and use a recon scalar workflow by @tsalo in https://github.com/PennLINC/qsirecon/pull/79
* [WIP] Make a system for keeping docs and file names in sync by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/86
* Convert pipeline configs from JSON to YAML by @tsalo in https://github.com/PennLINC/qsirecon/pull/84
* [DOCS] clean up by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/101
* Draft pre-init ingression by @tsalo in https://github.com/PennLINC/qsirecon/pull/102
* [ENH] Update AMICO by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/115
* [FIX] mif2fib by @ameliecr in https://github.com/PennLINC/qsirecon/pull/116
* Fix how bundles to be tracked are selected for DSIstudio autotrack by @ameliecr in https://github.com/PennLINC/qsirecon/pull/121
* [FIX] workflow connection in dsi_studio_gqi by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/142
* [CI]  add hsvs test by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/136
* [FIX] dsi_studio_gqi workflow connect by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/146
* [DOC] Minor addition for skipping connectivity matrices step by @chiuhoward in https://github.com/PennLINC/qsirecon/pull/150
* Add page documenting output structure by @tsalo in https://github.com/PennLINC/qsirecon/pull/156
* Add information about QSIPrep/QSIRecon releases by @tsalo in https://github.com/PennLINC/qsirecon/pull/158
* [CI] Add tests for reading pre-1.0 outputs from qsiprep by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/155
* [ENH] Support outputs from qsiprep 1.0.0rc0 by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/160
* [FIX] get rid of logging error #145 by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/161
* Add UKB ingression by @smeisler in https://github.com/PennLINC/qsirecon/pull/147
* [FIX] set TMPDIR before running plot_peaks by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/163
* [ENH] match to qsiprep nipype/nireports versions by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/167
* Add in Val's text for connectivity matrices by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/173
* Disable test_main in the CI integration tests by @mattcieslak in https://github.com/PennLINC/qsirecon/pull/177

### New Contributors

* @tsalo made their first contribution in https://github.com/PennLINC/qsirecon/pull/1
* @mattcieslak made their first contribution in https://github.com/PennLINC/qsirecon/pull/57
* @cookpa made their first contribution in https://github.com/PennLINC/qsirecon/pull/91
* @dependabot made their first contribution in https://github.com/PennLINC/qsirecon/pull/100
* @ameliecr made their first contribution in https://github.com/PennLINC/qsirecon/pull/116
* @chiuhoward made their first contribution in https://github.com/PennLINC/qsirecon/pull/150

**Full Changelog**: https://github.com/PennLINC/qsirecon/commits/1.0.0