Merge tag '23.1.0'

23.1.0 (June 12, 2023)

New feature release in the 23.1.x series.

This release substantially reworks the resampling to fsLR grayordinate space,
better accounting for partial volumes and high variance voxels. If you are
resampling using ``--project-goodvoxels``, we strongly recommend upgrading.

Fieldmap handling is improved, with better preference given to single-band
references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will
no longer estimate fieldmaps that are not intended to be used to correct BOLD
series, reducing unneeded processing.

This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA,
set ``MNI152NLin6Asym:res-2`` as a target output space. MELODIC and ICA-AROMA
can be run on the resulting images in a separate pipeline. For further
information on the reasoning behind this change, see
`GitHub issue #2936 <https://github.com/nipreps/fmriprep/issues/2936>`__.

This release increments the versions of ANTs and FSL bundled in the Docker
image.

With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions
in fMRIPrep and SDCflows.

* FIX: Raise RuntimeError at build if echos have mismatched shapes (#3028)
* FIX: Inconsistent fmapless estimation when ignoring fieldmaps (#2994)
* FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (#2986)
* FIX: Estimate free memory with "available", not "free" (#2985)
* ENH: Add ``--me-t2s-fit-method`` parameter (#3030)
* ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (#3011)
* ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (#3008)
* ENH: Remove ICA-AROMA from workflow and docs (#2966)
* RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (#3025)
* MNT: Update ANTs pin in Docker image (#3016)
* MNT: Update governance docs (#2992)
* MNT: Refactor Docker build process (#2982)
* MNT: Pin conda environment more strictly (#2853)
* MNT: Require niworkflows ~1.3.6 (#2740)
* CI: Use registry for layer caching (#3012)
* CI: Upgrade docker orb (#2865)

Author: effigies

CHANGES.rst

@@ -1,5 +1,49 @@
+23.1.0 (June 12, 2023)
+======================
+New feature release in the 23.1.x series.
+
+This release substantially reworks the resampling to fsLR grayordinate space,
+better accounting for partial volumes and high variance voxels. If you are
+resampling using ``--project-goodvoxels``, we strongly recommend upgrading.
+
+Fieldmap handling is improved, with better preference given to single-band
+references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will
+no longer estimate fieldmaps that are not intended to be used to correct BOLD
+series, reducing unneeded processing.
+
+This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA,
+set ``MNI152NLin6Asym:res-2`` as a target output space. MELODIC and ICA-AROMA
+can be run on the resulting images in a separate pipeline. For further
+information on the reasoning behind this change, see
+`GitHub issue #2936 <https://github.com/nipreps/fmriprep/issues/2936>`__.
+
+This release increments the versions of ANTs and FSL bundled in the Docker
+image.
+
+With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions
+in fMRIPrep and SDCflows.
+
+* FIX: Raise RuntimeError at build if echos have mismatched shapes (#3028)
+* FIX: Inconsistent fmapless estimation when ignoring fieldmaps (#2994)
+* FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (#2986)
+* FIX: Estimate free memory with "available", not "free" (#2985)
+* ENH: Add ``--me-t2s-fit-method`` parameter (#3030)
+* ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (#3011)
+* ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (#3008)
+* ENH: Remove ICA-AROMA from workflow and docs (#2966)
+* RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (#3025)
+* MNT: Update ANTs pin in Docker image (#3016)
+* MNT: Update governance docs (#2992)
+* MNT: Refactor Docker build process (#2982)
+* MNT: Pin conda environment more strictly (#2853)
+* MNT: Require niworkflows ~1.3.6 (#2740)
+* CI: Use registry for layer caching (#3012)
+* CI: Upgrade docker orb (#2865)
+
+
 23.0.2 (April 24, 2023)
 =======================
+Bug fix release in the 23.0.x series.
 
 This release fixes issues with `_phase1+2`, `_phasediff` and `_fieldmap`
 fieldmap files that are found with an orientation other than RAS.

requirements.txt

@@ -33,13 +33,13 @@ click==8.1.3
     #   codecarbon
     #   nipype
     #   pybids
-codecarbon==2.2.1
+codecarbon==2.2.3
     # via fmriprep (pyproject.toml)
 contourpy==1.0.7
     # via matplotlib
 cycler==0.11.0
     # via matplotlib
-cython==0.29.34
+cython==0.29.35
     # via nitime
 docopt==0.6.2
     # via num2words
@@ -59,7 +59,7 @@ h5py==3.8.0
     # via nitransforms
 idna==3.4
     # via requests
-imageio==2.28.1
+imageio==2.31.0
     # via scikit-image
 indexed-gzip==1.7.1
     # via smriprep
@@ -82,7 +82,7 @@ lazy-loader==0.2
     # via scikit-image
 lockfile==0.12.2
     # via smriprep
-looseversion==1.1.2
+looseversion==1.2.0
     # via
     #   fmriprep (pyproject.toml)
     #   nipype
@@ -95,7 +95,7 @@ lxml==4.9.2
     #   svgutils
 mapca==0.0.3
     # via tedana
-markupsafe==2.1.2
+markupsafe==2.1.3
     # via jinja2
 matplotlib==3.7.1
     # via
@@ -143,7 +143,7 @@ nitransforms==22.0.0
     #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.7.9
+niworkflows==1.8.0
     # via
     #   fmriprep (pyproject.toml)
     #   sdcflows
@@ -188,7 +188,7 @@ packaging==23.1
     #   niworkflows
     #   scikit-image
     #   smriprep
-pandas==2.0.1
+pandas==2.0.2
     # via
     #   codecarbon
     #   fmriprep (pyproject.toml)
@@ -258,7 +258,7 @@ requests==2.31.0
     #   fmriprep (pyproject.toml)
     #   nilearn
     #   templateflow
-scikit-image==0.20.0
+scikit-image==0.21.0
     # via
     #   niworkflows
     #   sdcflows
@@ -281,11 +281,11 @@ scipy==1.10.1
     #   scikit-learn
     #   sdcflows
     #   tedana
-sdcflows==2.4.3
+sdcflows==2.5.1
     # via fmriprep (pyproject.toml)
 seaborn==0.12.2
     # via niworkflows
-sentry-sdk==1.24.0
+sentry-sdk==1.25.1
     # via fmriprep (pyproject.toml)
 simplejson==3.19.1
     # via nipype
@@ -294,7 +294,7 @@ six==1.16.0
     #   apscheduler
     #   isodate
     #   python-dateutil
-smriprep==0.11.1
+smriprep==0.12.0
     # via fmriprep (pyproject.toml)
 sqlalchemy==2.0.15
     # via pybids
@@ -327,7 +327,7 @@ traits==6.3.2
     #   sdcflows
 transforms3d==0.4.1
     # via niworkflows
-typing-extensions==4.6.0
+typing-extensions==4.6.3
     # via
     #   bokeh
     #   formulaic
@@ -336,7 +336,7 @@ tzdata==2023.3
     # via pandas
 tzlocal==5.0.1
     # via apscheduler
-urllib3==1.26.16
+urllib3==2.0.3
     # via
     #   requests
     #   sentry-sdk

wrapper/src/fmriprep_docker/__main__.py

@@ -41,7 +41,7 @@
 MISSING = """
 Image '{}' is missing
 Would you like to download? [Y/n] """
-PKG_PATH = '/opt/conda/lib/python3.9/site-packages'
+PKG_PATH = '/opt/conda/envs/fmriprep/lib/python3.10/site-packages'
 TF_TEMPLATES = (
     'MNI152Lin',
     'MNI152NLin2009cAsym',