What’s new
22.0.0 (July 28, 2022)
New feature release in the 22.0.x series.
This release has been tested to work with Python 3.9 and FreeSurfer 7.2, which are now bundled in the Docker image.
This release also features improvements to T2* and carpetplot reporting.
For the next release, we are investigating issues with susceptibility distortion correction (SDC). Please check your results carefully and report any issues you find.
FIX: Update wrapper python path (#2783)
FIX: Preserve
collect_data
behavior by using named args (#2754)FIX: Update fMRIPrep version in bibliography at run time (#2738)
FIX: Plot carpetplot with CIFTI-specific colorbar (#2737)
FIX: Two minor typos in report spec (#2708)
ENH: Clip T2* values at 100ms to keep consistent histogram axes (#2781)
ENH: Plot histogram of T2* values in gray-matter mask (#2778)
ENH: Save T2starmap files in all requested output spaces, if calculated (#2776)
ENH: Compare T2* map to BOLD reference (#2751)
ENH: Add edge-regressors to confounds & crown to carpetplot (#2621)
ENH: Add major/minor versions to base workflow name (#2716)
DOC: Fix JSON typo in config in FAQ (#2771)
DOC: Clarify calculation of confounding signals (#2724)
MNT: Build on Python 3.9 environment (#2782)
MNT: Seed ignore-revs file and script to tag new hashes with log entries (#2748)
MNT: Require PyBIDS 0.15+ to allow fMRIPrep to preserve zero-padding in run entity (#2745)
MNT: Upload artifacts after each step of Circle’s workflow (#2736)
MNT: Normalize code style of
workflows.confounds
(#2729)MNT: Ask for fmriprep-docker RUNNING line (#2670)
DOCKER: Bundle FreeSurfer 7 (#2779)
CI: Touch up CircleCI configuration (#2764)
CI: Update package builds to use python -m build (#2746)
21.0.2 (April 21, 2022)
Bug-fix releaase in the 21.0.x series.
This release includes a few bug-fixes for susceptibility distortion correction (SDC) and multi-echo (ME). A few notable fixes include: - Added tolerance for affine precision differences when using EPI fieldmaps. - Removed hang-ups when reusing anatomical derivatives with ME data. - Increased BOLD masking workflow robustness.
A full list of changes can be found below:
DOCKER: Update multiarch deb package link (#2758)
ENH: Add affine_tolerance flag to MergeSeries (nipreps/niworkflows#706)
FIX: Initialize BIDS layout after cleaning working directory (#2741)
FIX: Avoid double unwarping during resampling of processed multi-echo data (#2730)
FIX: Account for potential lists of lists in multi-echo cases (nipreps/niworkflows#719)
FIX: Improve reliability of BOLD masking workflow (nipreps/niworkflows#712)
FIX: Relax tolerance for different affines when concatenating blips (nipreps/sdcflows#265)
21.0.1 (January 24, 2022)
Bug-fix release in the 21.0.x series.
This release re-enables reverse-PE EPI fieldmaps, i.e. EPIs acquired with the
opposite phase-encoding direction to a BOLD series.
Additionally, the --use-syn-sdc
option will now error by default if no
PhaseEncodingDirection
can be found for a BOLD series. To reduce this to
a warning, use --use-syn-sdc warn
. SyN-SDC will NOT be run, but the workflow
will proceed.
Note
topup
runtime scales with the number of volumes used, so fMRIPrep defaults to
using a maximum of 5 volumes from each of the BOLD series and the EPI fieldmap.
To adjust this, please use the --topup-max-vols
parameter.
FIX: Create single fmap_select_std node for use with all ANAT estimators (#2692)
FIX: Re-enable reverse-PE EPI fieldmaps (#2684)
FIX: Pass boolean use_syn_sdc to find_estimators (#2685)
FIX: Ensure AROMA inputs are uncompressed if –low-mem (#2657)
ENH: Add
--topup-max-vols
flag to control TOPUP runtime (#2688)ENH: Allow
--use-syn-sdc
to take a “warn” option to avoid exiting when PE dir is unavailable (#2680)RF: Add extension field to differentiate from upcoming templates (#2613)
WRAPPER: Map
--bids-filter-file
s into Docker container (#2691)MNT: Silence warning from pybids; list packaging as dependency (#2689)
MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)
MNT: Restore nitime to requirements, necessary for DVARS (#2678)
21.0.0 (December 14, 2021)
A new series is finally here!
Some highlights of this version’s new features include a substantial rework of fMRIPrep’s
susceptibility distortion correction (including the addition of FSL’s topup
as the new
default PEPOLAR correction technique), improved flexibility for multiecho scans, and
dependency version upgrades within the Docker environment.
Note
To follow BIDS Derivatives more closely, fMRIPrep’s default output layout has changed.
To enable the legacy layout, use the --output-layout legacy
flag.
For more information, please see https://fmriprep.org/en/latest/outputs.html#layout
Caution
As with all minor version increments, working directories from previous versions should not be reused.
Thank you for using fMRIPrep! If you encounter any issues with this release, please let us know by posting an issue on our GitHub page!
A full list of changes can be found below.
DOC: Remove mention to
epidewarp.fsl
fromNOTICE
(#2629)DOC: Update description of output layout, add discussion of legacy mode (#2646)
DOC: ME | Add missing output to documentation, improve boilerplate (#2608)
DOC: Add –index-metadata to
pybids layout
faq (#2546)DOC: Add warning about slice timing correction in output documentation. (#2502)
DOC: Update sample report (#2519)
DOC: Refactor README and citing information (#2474)
DOC: Point documentation at SDCFlows and remove SDC section (#2470)
DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
DOC: Better explanation on how spike regressors are generated (#2465)
DOC: Clarify that
res-2
entity does not mean 2mm (#2466)DOC: adds –mem metavar (#2378)
DOC: skull stripping is forced by default (#2345)
DOCKER: Shrink Docker image size (#2551)
DOCKER: Strip ABI tag from libQt5Core.so.5 to prevent Singularity failures (#2535)
ENH: Make bids the default output layout option (#2555)
ENH: Mask multi-echo data with reference mask instead of echo-specific masks (#2349)
ENH: Replace initial FLIRT with mri_coreg, use -basescale 1 for FLIRT-BBR (#2625)
ENH: Add flag for STC reference time and set in all cases (#2520)
ENH: Use
BIDSLayoutIndexer
and do not index unnecessary modalities (#2494)ENH: Allow users to download templateflow templates to directory (#2482)
ENH: Detect 3D & too-short BOLD series, warn and skip run’s workflow building (#2461)
ENH: Modernize Dockerfile (#2409) (#2270)
ENH: Leverage SDCFlows 2.x API (#2392)
ENH: Tedana-friendly ME derivatives (#2575)
ENH: Better integration of SDCFlows’ unwarping (#2576)
ENH: Refactor workflow to adopt SDCFlows’ new correction workflow (#2547)
FIX: Threshold boldref resampled values to be non-negative (#2630)
FIX: Restore SyN-SDC (#2530)
FIX: Confusing I/O field
bold_mask
in bold-to-bold resampling workflow (#2611)FIX: ME | Revise SDC compute graph (#2610)
FIX: Propagate the SDC warp to resampling node also with ME (#2609)
FIX: Optimize build job on CircleCI (#2605)
FIX: Minor multiecho issues (#2574)
FIX: Missing numpy import (#2533)
FIX: Avoid eager imports from NiWorkflows causing API breaks (#2495)
FIX: Split aCompCor into aCompCor, cCompCor, wCompCor (#2523)
FIX: Avoid unnecessary connections based on branching logic (#2508)
FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
FIX: Simplify STC logic for too short BOLD series (#2489)
FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
FIX:
DerivativesDataSink
nondeterministic checksums fixed withniworkflows=~1.3.4
(#2458)FIX: Address dependency incompatibilities by pinning specific packages (#2463)
FIX: Unprotected import of
sentry_sdk
, which is not a dependency (#2460)FIX: Clarify phase encoding direction, rather than axis (#2302)
MAINT: Conform fast-track outputs to BIDS ordering (#2663)
MAINT: Reduce redundant processing of ds005 (#2649)
MAINT: Finalize the work we started with the refactor of the Docker image (#2601)
MAINT: Run full workflows on tags (#2593)
MAINT: Stage Python environment of Docker image from nipreps/miniconda (#2581)
MAINT: Stop NeuroDebian dependency in Dockerfile (#2578)
MAINT: Run pytest through GitHub actions (#2529)
MAINT: Relicense +20.3.x - BSD-3-Clause -> Apache License 2.0 (#2325)
MAINT: Add missing OASIS30 WM/BS probsegs (#2471)
MAINT: Update BIDS validator to 1.8.0 (#2443)
MAINT: Address the problems of a sloppy merge (#2468)
MAINT: Containers - remove
/root/.npm
(#2464)MAINT: Remove traces of Xenial base (#2459)
MAINT: Revise CircleCI’s cache tags to avoid mixups between builds (#2457)
MAINT: Back port CircleCI configuration from dev branch (#2456)
MAINT: Increase minimum tedana version (#2366)
MAINT: Docker hub has disabled password authentication (#2448)
MAINT: Add Lea Waller to
contributors.json
(#2304)MAINT: Move away from nearly deprecated images (#2295)
MAINT: Migrate from poldracklab to nipreps orgs (#2290)
MAINT: Ease CI packaging tests (#2472)
RF/FIX: Iterate over echo indices, not filenames, simplifying iteration logic (#2651)
20.2.7 (January 24, 2022)
Bug-fix release in the 20.2.x LTS series.
FIX: Clarify phase encoding direction, rather than axis (#2690)
FIX: Ensure AROMA inputs are uncompressed if –low-mem (#2657)
FIX: Add
-basescale 1
parameter to avoidflirt
scaling (#2624)WRAPPER: Map
--bids-filter-file
s into Docker container (#2691)MNT: Add netbase to Docker image to ensure correct datalad operation (#2682)
20.2.6 (October 27, 2021)
Patch release in the 20.2.x LTS series.
This release includes an updated runtime environment for Docker/Singularity users.
This environment includes a newer release of indexed_gzip
,
fixing CrcError
s previously encountered.
CI: Run full workflows on tags (#2593)
RF: Add extension field to differentiate from upcoming templates (#2613)
20.2.5 (October 12, 2021)
Bug-fix release in the 20.2.x LTS series.
This release includes a fix to --slice-time-ref
parsing. Also, some
issues in anatomical processing are resolved, including poorly-interpolated
labels in aseg segmentations, and probabilistic segmentations have reverted
to FAST.
FIX: –slice-time-ref option parsing (#2573)
CI: Add style checks (missing since Travis got throttled) (#2570)
20.2.4 (October 04, 2021)
Bug-fix release in the 20.2.x LTS series.
This release includes some fixes to minor bugs, and includes enhancements to allow the user to specify a different slice-timing-correction (STC) target.
Each BOLD series will contain SliceTimingCorrected
metadata to indicate
whether STC was performed. If performed, the StartTime
metadata field will
be set to indicate the onset time of the BOLD series.
FIX: Avoid unnecessary connections based on branching logic (#2508)
FIX: Permit missing TR to show PyBIDS error at workflow construction time (#2513)
[BACKPORT] FIX: Catch FreeSurfer error related to FIPS being enabled (#2490)
ENH: Use
BIDSLayoutIndexer
and do not index unnecessary modalities (#2494)[BACKPORT] ENH: Slice-timing correction improvements (#2565)
20.2.3 (July 21, 2021)
Patch release in the 20.2.x LTS series. Addresses minimal problems in some edge-cases, overall improves the documentation and infrastructure. Exercises some maintenance operations addressing problems surfaced when the previous tag 20.2.2 was released.
FIX: Address the problems of a sloppy merge (#2468)
FIX:
DerivativesDataSink
nondeterministic checksums fixed withniworkflows=~1.3.4
(#2458)FIX: Address dependency incompatibilities by pinning specific packages (#2463)
FIX: Unprotected import of
sentry_sdk
, which is not a dependency (#2460)ENH: Detect 3D & too-short BOLD series, warn and skip run’s workflow building (#2461)
DOC: Transfer duplicated documentation to www.nipreps.org (#2469)
DOC: Better explanation on how spike regressors are generated (#2465)
DOC: Clarify that
res-2
entity does not mean 2mm (#2466)MAINT: Containers - remove
/root/.npm
(#2464)MAINT: Back port CircleCI configuration from dev branch (#2456)
20.2.2 (July 16, 2021)
Hot-fix release in the 20.2.x LTS series. Addressing a bug on fMRIPrep’s resampling to standard spaces (#2444). In addition, some other relevant bug-fixes and performance improvements are built in this patch.
FIX: Feed NiTransforms with LTAs of type RAS2RAS (#2444)
FIX: Add some clarity to
BrokenProcessPool
failures (#2436)FIX: Fall-back to initializing workflow in main process (#2435)
FIX: Raise informative error when duplicate subworkflows are added (#2434)
FIX: Non-existing path or JSON syntax error for
--bids-filter-file
should raise on error (#2331)FIX: Ignore SBRef files if
--ignore sbref
is passed (#2370)ENH: Relax requirement for PyBIDS databases to exist (#2429)
ENH: Improve
_get_series_len
performance (#2406)ENH: Set and track NumPy’s random seed (#2400)
DOC: Skull-stripping is forced by default (#2430)
MAINT: Pin
nilearn==0.6.2
(#2427)MAINT: Pin
tedana==0.0.9a1
for LTS branch (#2403)MAINT: Failing CI (#2401)
20.2.1 (November 06, 2020)
Bug-fix release in the 20.2.x LTS series.
This release adds missing metadata to GIFTI and CIFTI-2 derivatives and fixes a logging bug affecting a small number of datasets.
Additionally the --output-layout bids
flag will now output fMRIPrep derivatives directly
into the output directory, nesting FreeSurfer derivatives by default in
<output>/sourcedata/freesurfer
. This layout allows the output root to be a valid BIDS
Derivatives dataset, simplifying data management and provenance tracking with content tracking
tools, such as DataLad. This layout will likely become the
default in future release series.
ENH: Output TaskName and timing metadata for all resampled BOLD series (#2320)
ENH: Add
--output-layout
CLI option to enable BIDS (YODA) mode (#2303)ENH: Add Docker authentication to increase pull rate limit (#2316)
FIX: Specify logger for warning (#2298)
20.2.0 (September 28, 2020)
With this third minor release series of 2020, the first fMRIPrep LTS (long-term support) is finally here!
This release contains a number of bug-fixes and enhancements mostly related to easing the maintenance, anticipating patch-release breaking changes to ensure a longstanding LTS, and addressing some run-to-run repeatability problems of the CompCor implementation.
Long-Term Support (LTS)
fMRIPrep 20.2 LTS introduces the long-term support program. This LTS version will be kindly steered and maintained by the group of Dr. Basile Pinsard and Prof. Pierre Bellec at CRIUGM, (Université de Montréal). The LTS is planned for a window of 4 years of support (i.e., until September 2024).
Caution
As with all minor version increments, working directories from previous versions should not be reused.
Thank you for using fMRIPrep! If you encounter any issues with this release, please let us know by posting an issue on our GitHub page!
A full list of changes can be found below.
FIX: Pin NiWorkflows 1.3.1 and sMRIPrep 0.7.0rc2, including bugfix for INU-correction failures (nipreps/niworkflows#567)
FIX: Get missing
probseg
file from MNI152NLin2009cAsym (#2271)FIX: Restore
--ignore t2w/flair
options (#2260)FIX: Revise the reproducibility of CompCor masks (#2130)
FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (#2239)
FIX: Skip the T1w check if
--anat-derivatives
is provided. (#2201)FIX: Storing
--bids-filters
within config file (#2177)FIX: Revise multi-echo reference generation, permitting using SBRefs too (#1803)
FIX: FreeSurfer license manipulation & canary
ENH: Output CompCor masks if
--debug compcor
is passed (#2248)ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (#2223)
ENH: Reuse config (#2240)
ENH: Save BOLD-anatomical transforms to derivatives folder (#2233)
ENH: Leverage BIDSLayout’s
database_path
(#2203)ENH: Add
--no-tty
option tofmriprep-docker.py
(#2204)ENH: Report number of echoes in BOLD summary. (#2184)
ENH: Ensure NiPype telemetry is just pinged once (#2168)
DOC: Add FAQ entry for using pre-indexed layouts (#2256)
DOC: Update reference in “Refinement of Brain Mask” description (#2215)
DOC: List TemplateFlow templates that need to be prefetched (#2196)
DOC: Update references to https://github.com/nipreps (#2191)
DOC: Pin NiPype with new Sphinx extension syntax (#2092)
MAINT: Upgrade ANTs to 2.3.3 in
Dockerfile
(9512086)MAINT: Track #2269 and #2269, bug-fixes on the 20.1.x series
MAINT: Remove derivatives from layout index ignores (#2258)
MAINT: Track #2252 from 20.1.x series (#2253)
MAINT: Silence PyBIDS warning by setting extension mode (#2250)
MAINT: Drop CircleCI docs build (#2247)
MAINT: Pin latest NiPreps (#2244)
MAINT: Update
setup.cfg
(flake8 and pytest) (#2183)MAINT: Delete release-drafter (#2169)
MAINT: Track bug-fix release on the 20.1.x series (#2165)
MAINT: Remove auto-comment bot (#2166)
MAINT: Improve the questions on the bug-report template (#2158)
20.1.4 (July 16, 2021)
Hotfix release addressing a bug on fMRIPrep’s resampling to standard spaces. This release also includes some maintenance changes handling old versions of software.
FIX: Feed NiTransforms with LTAs of type RAS2RAS (#2444)
MAINT: Pin
svgutils==0.3.1
for the 20.1.x series (#2450)MAINT: Keep pip and setuptools with support for Python 3.5 (#2449)
MAINT: Some dependencies cannot be left unpinned (#2446)
20.1.3 (September 15, 2020)
Bug-fix release in the 20.1.x series.
FIX: Dependency conflict between NiWorkflows and TemplateFlow (#2269)
FIX: More targetted TemplateFlow queries to work with all later releases (#2268)
MAINT: Update dependency pinnings including
niworkflows~=1.2.9
and three minimal bug-fixes.
20.1.2 (September 04, 2020)
Bug-fix release in the 20.1.x series.
FIX: Revise confounds in confounds-correlation plots (#2252)
FIX: Coerce license path to pathlike (#2180)
DOC: Update new sMRIPrep location (#2211)
20.1.1 (June 04, 2020)
Bug-fix release in the 20.1.x series.
FIX: FreeSurfer license manipulation & canary (#2165)
FIX: Dismiss
echo
entity from SDC reports (#2160)FIX: Ensure the command-line alias of
--nprocs
is respected (#2152)MAINT: Use legacy pip/setuptools for py2 checking (#2156)
20.1.0 (May 27, 2020)
The second minor release series of 2020 is finally here!
fMRIPrep 20.1.0 introduces a magnitude of new features and improvements. Originally nominated to become the first LTS (long-term support) version of fMRIPrep, this release has been supercharged with many new features and bug-fixes. To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment. Some key additions in this release include:
A centralized configuration module keeping track of fMRIPrep’s many options and run-time and environmental circumstances and settings. The new config module, which has been also propagated to other NiPreps (dMRIPrep, MRIQC), comes to robustify the run-to-run replicability of fMRIPrep (e.g., tracking random seeds), make the option handling more modular but consistent (e.g., setting the ground for a command-line interface built off of the config module), and ease troubleshooting and telemetry.
The anatomical preprocessing fast-track: a new experimental command-line option (
--anat-derivatives <PATH>
) checks that all necessary anatomical derivatives required by fMRIPrep are present under<PATH>
, and skips the anatomical processing in full if fMRIPrep’s expectations are met. Because now functional processing of many sessions and runs can be efficiently split into more digestible computational units (i.e., cluster job) while guaranteeing the exact same anatomical results are being used, this can significantly speed up longitudinal study preprocessing, and it is a fundamental optimization to process databases of densely scanned individuals such as My Connectome. This option is not recommended for single-session processing.A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.
Thanks
With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.
New Paper!
This release comes after our latest protocol paper “Analysis of task-based functional MRI data preprocessed with fMRIPrep” has been accepted. The protocol describes how to use fMRIPrep on high-performance clusters to preprocess fMRI data for task-based analyses. Please check out the latest version on Nature Protocols or the preprint.
Caution
As with all minor version increments, working directories from previous versions should not be reused.
Thank you for using fMRIPrep! If you encounter any issues with this release, please let us know by posting an issue on our GitHub page!
A full list of changes can be found below.
FIX:
MultiLabel
interpolations should not usefloat=True
(#2147)FIX: Generate proper LTA transform prior BOLD sampling on surfaces (#2146)
FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
FIX: Dismiss
echo
entity on several derivatives and figures outputs (#2133)FIX: Correct summary report when using previously run
recon-all
(#2124)FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
FIX: Explicitly add default
native
resolution to volumetric outputs (nipreps/niworkflows#494)ENH: Finish the upstreaming of NiTransforms interfaces to NiWorkflows (#2132)
ENH: Enable filtering for
ANY
orNONE
in--bids-filter-file
(#2123)ENH: Use new
DerivativesDataSink
from NiWorkflows 1.2.0 (#2114)ENH: Config module (#2018)
ENH: Add option to ignore T2w / FLAIR images (#2015)
ENH: Ensure subcortical volume in CIFTI is in LAS orientation (nipreps/niworkflows#484)
ENH: Add option to skip brain extraction (#2039)
ENH: Use CIFTI sampling for carpetplot when available (#2055)
MAINT: Stop printing full boilerplate,
black fmriprep/cli
(#2119)MAINT: Ensure YAML loader is specified (#2125)
MAINT: PIN tedana version (#2117)
MAINT: Bump minimum Python to 3.7 (#2017)
MAINT: Remove unused console scripts (#2048)
MAINT: Reduce the overall size of outputs (nipreps/niworkflows#492)
DOC: Update parallel subject neurostars link in FAQ (#2104)
DOC: Add FAQ about reusing work directory (#2045)
20.0.x series (February 2020)
20.0.7 (May 5, 2020)
Bug-fix release in the 20.0.x series.
This release includes a new, portable version of the templateflow python client. This includes an automatic check to fetch the latest templateflow templates every time.
MAINT: Bump templateflow to auto-update template skeleton
20.0.6 (April 16, 2020)
Bug-fix release in the 20.0.x series.
This release fixes a bug for phase-difference fieldmaps that are not in RAS+ orientation. The bug presented as an error if the orientation was reordered relative to RAS+ (for example, AIL+) and the swapped dimensions were not of the same size. Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle if the original orientation was LAS+. Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not currently considered problematic.
This bug affects all earlier versions of fMRIPrep, except for 1.5.10 and any future releases in the 1.5.x series.
FIX: Do not reorient magnitude images (nipreps/sdcflows#98)
20.0.5 (March 19, 2020)
Bug-fix release in 20.0.x series.
With thanks to James Kent for the fix and Blaise Frederick for the report and testing.
FIX: Add CE agent to output figure filename templates (nipreps/niworkflows#482)
20.0.4 (March 17, 2020)
A bug-fix release improving documentation for filtering BIDS files and standardizing CIFTI volume orientation.
With thanks to Ursula Tooley for the contribution.
DOC: FAQ section for BIDS filter (#2028)
FIX: Ensure BOLD and label orientations are equal (nipreps/niworkflows#477).
20.0.3 (March 12, 2020)
A bug-fix release for CIFTI surfaces.
This release remedies a resampling error when generating fsLR surfaces that was producing erroneous CIFTI files. We strongly recommend all users who have generated CIFTI output with previous 20.0.x releases to upgrade and rerun.
FIX: Remedy fsLR surface resampling (#2032)
20.0.2 (March 6, 2020)
A bug squashing release in the 20.0.x series.
This release fixes the use of custom templates within the docker wrapper, remedies crashes when FreeSurfer HOME was not set, and improves the documentation for local installations.
With thanks to Blaise Frederick for the contribution.
DOC: Update standalone installation requirements (#2009)
FIX: Crashes whenever FREESURFER_HOME is not set (#2014)
FIX: Local template mounting (wrapper) (#2020)
MAINT: Pin minor series of nipype, major series of nibabel (#2021)
20.0.1 (February 27, 2020)
Bug-fix release in 20.0.x series.
This release includes fixes for rare images with invalid qform matrices and some minor improvements in report readability and inclusion of common templates in the Docker image.
FIX: Handle qforms with invalid quaternions (nipreps/niworkflows#466)
FIX: update niworkflows location (#2005)
ENH: Display errors as summary/details elements in reports (nipreps/niworkflows#464)
DOC: Add
--fs-subjects-dir
usage to slurm example (#2003)CI: Test that Docker image can run a common set of output spaces without network access (#1997)
20.0.0 (February 24, 2020)
The major release of 2020 is here!
fMRIPrep is transitioning to a calendar version system (#1912). The CalVer system reflects fMRIPrep’s nature as an evolving workflow and does not impose any artificial incentive for “big-change” releases. It also permits to quickly see how out-of-date someone’s version is. As of now, the default version increment is the minor release number. Hence, when the minor release number changes the work directory of fMRIPrep will presumably break. Micro releases only include bug-fixes that can reuse exiting working directories.
The major highlight of this release entails CIFTI generation to match
HCP grayordinates.
In addition, the new fMRIPrep 20.0.0 has gone through a major overhaul in the
handling of standard spaces (spatial normalizations, fusion of prior knowledge from
corresponding atlases) and imaging outputs.
In particular, the new series almost completely implements the new
syntax for --output-spaces
to describe the (non)standard spatial references
that shall be used for generating outputs
(#1604).
This release includes contributions from Azeez Adebimpe and Basile Pinsard - very much appreciated.
ENH: Warn when existing output version does not match current pipeline version (#1967)
ENH: Add
--clean-workdir
argument (#1966)ENH: Refactor of how spatial normalization targets and
--output-spaces
are maintained (#1955) (#1983)ENH: Add
--bids-filter-file
argument for more controlled data querying (#1770)FIX: Ensure subject ID is used when selecting BIDS data (#1982)
FIX: Display a log message when processing completes successfully (#1977)
DOC: Clean up surface outputs (#1993)
DOC: Integrate intersphinx, drop external module wrapping (#1989)
DOC: Improve custom template usage description (#1969)
MAINT: Use local docker registry (#1990)
MAINT: Pin connectome-workbench 1.3.2, add to documented dependencies (#1958)
MAINT: Pin NiBabel, NiWorkflows, sMRIPrep (#1971)
MAINT: CI build error fixes (#1976)
1.5.x series (September 2019)
1.5.10 (April 16, 2020)
Bug-fix release in the 1.5.x series.
This release fixes a bug for phase-difference fieldmaps that are not in RAS+ orientation. The bug presented as an error if the orientation was reordered relative to RAS+ (for example, AIL+) and the swapped dimensions were not of the same size. Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle if the original orientation was LAS+. Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not currently considered problematic.
This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5.
FIX: Do not reorient magnitude images (nipreps/sdcflows#98)
1.5.9 (February 14, 2020)
Bug-fix release in the 1.5.x series.
This release fixes a bug for some phase maps generated by Philips. A full fix with better handling of all phase maps will be available in an upcoming minor release (20.0 or 20.1), but this should permit users who are processing with 1.5.x to resolve this issue in a way that does not affect phase maps unaffected by the bug.
FIX: Center phase maps around central mode, avoiding FoV-related outliers (nipreps/sdcflows#89)
1.5.8 (January 28, 2020)
Bug-fix release in the 1.5.x series.
FIX: SyN SDC logic failing in
--force-syn
cases (#1951)
1.5.7 (January 23, 2020)
Bug-fix release in the 1.5.x series.
This release fixes a bug specifically for T1w images with dimensions ≤256 voxels but a field-of-view >256mm.
FIX: Calculate FoV with shape and zooms (nipreps/smriprep#161)
1.5.6 (January 22, 2020)
Bug-fix release in the 1.5.x series.
FIX: Include all functional runs in reports, establish consistent ordering (#1937)
FIX: Use SyN-SDC if –use-syn-sdc and –ignore fieldmaps are used (#1942)
1.5.5 (January 14, 2020)
Bug-fix release in the 1.5.x series.
FIX: Correctly select volumetric spaces for carpetplot (#1932) @effigies
FIX: Constrain setuptools for Python 2.7 installs of fmriprep-docker (#1933) @effigies
1.5.4 (December 18, 2019)
Bug-fix release in the 1.5.x series.
FIX: Integrate fix for nipreps/sdcflows#77 (pin niworkflows-1.0.3, sdcflows-1.0.3) @oesteban
1.5.3 (December 12, 2019)
The last patch release of the 1.5.x series containing features. As of 1.5.4, patch releases will only contain bug fixes, maintenance tasks and minor documentation revisions.
FIX: Do not run STC if SliceTiming metadata is set but empty (#1854) @oesteban
FIX: Link to EPINorm issue in README (#1903) @adelavega
FIX: Respect
--dummy-scans 0
(#1908) @jdkentENH: Upgrade SDCFlows to new API (1.0.0) (#1886) @oesteban
ENH: Add
--fs-subjects-dir
flag (#1901) @effigiesDOC: Improving accessibility of confounds description (#1877) @kfinc
MAINT: Ensure data is packaged in sdist (#1902) @effigies
MAINT: Remove deprecated command-line arguments (#1909) @mgxd
1.5.2 (December 2, 2019)
Bug-fix release in the 1.5.x series.
FIX: Ensure data type of masked image matches T1.mgz (nipreps/niworkflows#430) @effigies
1.5.1 (November 26, 2019)
After an arduous walk through release-candidates, release 1.5.1 includes a new release of Nipype which addresses the problems related to results files many users have been experiencing.
With thanks to Marc Bue, Alejandro De La Vega, Tailor Salo, Asier Erramuzpe and Soichi Hayashi.
FIX: Treat missing field maps as empty list instead of
None
(#1820) @tsaloFIX: Raise error if
work_dir
is a child ofbids_dir
(#1860) @adelavegaFIX: Change ICA-AROMA filenames to fit current naming scheme (#1861) @jdkent
FIX: Update code-server in the Dockerfile_devel (#1852) @erramuzpe
FIX: Do not generate
desc-smoothAROMAnonaggr_bold
conversions on standard spaces (#1838) @oestebanFIX: Skip plotting step of ICA-AROMA (#1834) @oesteban
FIX: Error during version check trying to access read-only file systems (#1830) @oesteban
FIX: Bad results files loads; PIN: nipy/nipype master (#1806) @effigies
FIX: Adding comma to outputnode in init_func_preproc_wf (#1795) @marcbue
FIX: Ignore sourcedata and derivatives when fetching data (#1788) @effigies
ENH: Added skip_citation_process flag to skip processing
citation.md
(#1876) @soichihENH: Restore
space-MNI152NLin6Asym
for AROMA denoised outputs (#1839) @oestebanENH: Confounds metadata (#1708) @rciric
DOC: Remove OpenNeuro badge (#1862) @adelavega
DOC: Improve documentation about TemplateFlow and Containers (#1802) @oesteban
DOC: Add
VERSION
argument to docker build instructions (#1797) @effigiesDOC: Revise docstrings of workflows for correct parsing with napoleon #1882 (@oesteban)
CI: Use recent Python image to build packages (#1790) @effigies
MAINT: Update to the new API of sMRIPrep (#1879) @adelavega
MAINT: Update
CONTRIBUTING.md
inspired by dMRIPrep’s (#1853) @oestebanMAINT: Enable circleci-artifacts-redirector (#1857) @effigies
MAINT: Cleaning up dependencies (#1832) @oesteban
MAINT: Pin Python 3.7.4 in CircleCI’s
build_docs
(#1836) @oestebanMAINT: Purge Cython and depend on SDCflows (#1792) @effigies
MAINT: Container images - cleanup
$HOME
in docker build (#1768) @oesteban
1.5.0 (September 9, 2019)
Two hallmark changes conducive to a new minor release line have been included in version 1.5.0: the upgrade of PyBIDS to the 0.9 series and the split of SDCflows off from fMRIPrep codebase. PyBIDS 0.9.x has a better handling of the indexed dataset that will permit some optimizations to fMRIPrep’s memory fingerprint. SDCflows now are found at nipreps/sdcflows, and have been split to allow a more granular and thorough testing in collaboration with M. Cieslak, A. Adebimpe, and T. Satterthwaite. Some other bugfixes, improvements to the documentation and minor features are also shipped with the new release. With thanks to Ursula Tooley, Sebastian Urchs and Gabriel A. Devenyi for contributions.
FIX: Minor improvements for templateflow installation in Docker images (#1764) @oesteban
FIX: Passing surface template keywords into carpetplot workflow (#1755) @oesteban
FIX: Postpone
pandoc
conversion of boilerplate after workflow has fully run (#1710) @oestebanFIX: Use MNI152NLin2009cAsym for SDC if no templates are specified (#1703) @effigies
FIX: Correct BOLD-T1w registration description if DoF != 9 (#1701) @effigies
ENH: Set up code-server docker recipe for interactive development (#1730) @jdkent
ENH: Make fmriprep print defaults for arguments with help (#1735) @gdevenyi
ENH: Add check for updates and check whether version has been flagged. (#1715) @oesteban
ENH: Add TaskName metadata to BOLD outputs (#1714) @effigies
REF: Separate SDCflows from fMRIPrep (#1670) @oesteban
DOC: Adding fMRIPrep benchmark info to FAQs (#1759) @surchs
DOC: Update
.zenodo.json
(#1732) @utooleyDOC: Add link to documentation in help of
--output-spaces
argument (#1722) @oestebanDOC: adding recon-all issue to faq (#1622) @franklin-feingold
DOC: Add copyright waiver to boilerplate and reviewer note to docs (#1691) @effigies
MAINT: niworkflows and nipype to use latest
N4BiasFieldCorrection
(#1752) @oestebanMAINT: Bump pybids and nipype dependencies (#1744) @effigies
MAINT: Move regression tests of EPI masks over to Niworkflows (#1716) @oesteban
MAINT: Remove old
extensions
entity selector for PyBIDS queries (#1707) @oestebanMAINT: Use PyBIDS 0.9.x via niworkflows/smriprep PRs (#1695) @effigies
1.4.x series (May 2019)
1.4.1 (July 9, 2019)
As of 1.4.1, the new infant and pediatric templates added to TemplateFlow are available to
brain extraction and spatial normalization.
Containers do not set the TEMPLATEFLOW_HOME
environment variable anymore, allowing
increased flexibility when running them (especially Singularity, for which the filesystem
is generally set read-only).
Additionally, BOLD files in native space can be generated and a minor bug related to the
handling of FreeSurfer outputs have been included.
FIX: Finalizing support for new templates and their command line modifiers (#1671) @oesteban
FIX: Do not set
TEMPLATEFLOW_HOME
(#1669) @oestebanFIX: FreeSurfer failed without adding some
fs*
to--output-spaces
(#1643) @oestebanENH: Show informative warning for phase1/2 type of fieldmaps (#1689) @oesteban
ENH: Allow template modifiers (a la
--output-spaces
) in skull-stripping (#1666) @oestebanENH: Write outputs in native-BOLD space (#1646) @oesteban
DOC: Add WHT to Zenodo (#1683) @wiheto
1.4.0 (May 15, 2019)
The new 1.4 series include several new features, several maintenance patches,
and numerous bugfixes.
The largest change to fMRIPrep’s interface is the new --output-spaces
argument that allows running spatial normalization to one or more standard
templates, and also to indicate that data preprocessed and resampled to the
individual’s anatomical space should be generated.
The implementation of this option will be completed in future releases to include
new nonstandard spaces (e.g., this BOLD run’s native space) and custom templates
providing a path.
For example, the following fMRIPrep options:
--template MNI152NLin6Asym --output-space template T1w fsaverage5 ----template-resampling-grid 2mm
now would be accomplished with:
--output-spaces MNI152NLin6Asym:res-2 anat fsaverage:den-10k
with the difference that more templates could be specified if needed, e.g.,
--output-spaces MNI152NLin6Asym:res-2 anat fsaverage:den-10k MNI152NLin2009cAsym:native
Related anatomical preprocessing workflows from sMRIPrep have gone through thorough revisions. In particular, the brain extraction workflow now is implemented in pure Nipype.
Users will notice the addition of two new subsections in the reports generated by fMRIPrep. The first addition describes the cumulative variance explained by successive a/tCompCor components. A second addition shows the correlations between the confounding regressors that fMRIPrep writes to the corresponding file, and their correlation to the global signal.
Series 1.4 increasingly relies on PyBIDS to handle not only inputs, but also outputs and reporting. The reports generation system has been deeply refactored to improve its generalizability across BIDS-Apps and addressing some rendering problems (e.g., when resizing ICA-AROMA components decompositions). Finally, there were several updates to packaging, testing and documentation, which should hopefully improve the experience for new users and contributors.
With thanks to Yaroslav Halchenko, Dan Lurie, Adriana Rivera-Dompenciel, Franklin Feingold, Markus Sneve, Anibal Heinsfeld, and James Kent for contributions.
FIX: Incorrect transforms being applied to aparc/asegs in standard space (#1636) @oesteban
FIX: Writing functional derivatives in standard spaces (#1632) @oesteban
FIX: Resampling of BOLD into standard spaces (#1627) @oesteban
FIX: Re-enable correct versioning within container (#1623) @oesteban
FIX: Update spline fitting distance for BOLD bias-field correction (#1603) @markushs
FIX: Mount Nipype config file under new
$HOME
(#1602) @oestebanFIX: Not having
template
as one--output-space
crashes fMRIPrep (#1560) @oestebanENH: Add
--dummy-scans
option (#1559) @jdkentENH: Reduce
BSplineFieldmap
memory usage (#1609) @effigiesENH: Confound model enhancement (#1487, #1586) @rciric
ENH: Allow multiple {non,}standard spaces (
--output-spaces
) (#1596) @oestebanENH: Switch to the refactored report generation from NiWorkflows (#1599) @oesteban
ENH: Force compression of derivative NIfTI volumes (#1600) @effigies
ENH: Do not allow writing derivatives directly into the BIDS root folder (#1589) @oesteban
ENH: Support 4D SBRefs when generating the bold reference (#1581) @oesteban
ENH: Remove pre-existing citation files before running (#1567) @yarikoptic
DOC: Improve appearance of parameter types in API docs (#1633) @anibalsolon
DOC: Confound enhancement documentation (#1625) @rciric
DOC: Add FAQ, Tips, Tricks section to RTD (cont. #1601) (#1610) @franklin-feingold
DOC: Companion of #1596 + punctual improvements of docs (#1605) @oesteban
DOC: Add examples/clarify
CONTRIBUTORS.md
(#1566) @jdkentDOC: Add
.bidsignore
requirement to docs on lesion masks (#1574) @danlurieDOC: Bump references of python3.6 to python3.7 (#1562) @jdkent
MAINT: Consolidate build configuration in
setup.cfg
(#1607) @effigiesMAINT: Progress bids-validator 1.2.3 (#1583) @yarikoptic
MAINT: Pin
nilearn!=0.5.0,!=0.5.1
to avoid problems plotting mgz images (#1585) @oestebanMAINT: Group all ‘finished running with errors’ sentry messages (#1552) @chrisgorgo
MAINT: Include hash of
dataset_description.json
in sentry metadata (#1553) @chrisgorgoCI: Reduce pointless expenditures (#1614) @effigies
CI: Use caches to pass data between jobs (#1608) @effigies
CI: Build docs outside of container (#1606) @effigies
CI: Fix label on CI step “Skipping doc building job” (#1564) @ariveradompenciel
1.3.x series (March 2019)
1.3.2 (March 18, 2019)
A new release providing better support for BIDS-Derivatives, an wrapping-up all the developments around TemplateFlow and stability of singularity images. With thanks to @sarenseeley for contributions.
ENH: Write derivatives metadata (#1546) @oesteban
DOC: Indicate that interpolation is NN above the EPI-to-T1w reportlet (#1542) @sarenseeley
1.3.1.post2 (March 13, 2019)
A hotfix release addressing issues related to TemplateFlow for Singularity users, via pinning templateflow>=0.1.2.
1.3.1.post1 (March 11, 2019)
A hotfix release addressing issues related to TemplateFlow for Singularity users.
FIX: Make sure
--cifti-output
requires at least one offsaverage{5,6}
(#1514) @oestebanFIX: Avoid using
$HOME
for storing templates (#1529) @chrisfilo
1.3.1 (March 6, 2019)
Updated ecosystem’s versions (TemplateFlow 0.1.x, Niworkflows 0.8.x, and sMRIPrep 0.1.x) to include latest improvements (bugfixes from niworkflows and the new pybids interface of templateflow). TemplateFlow 0.1.0 does not require datalad anymore. With thanks to @franklin-feingold for contributions.
UX: Reduce warning levels (#1513) @effigies
DOC:
fmriprep-docker
documentation (#1515) @franklin-feingoldREL: 1.3.1 (#1527) @oesteban
1.3.0.post3 (March 1, 2019)
Hotfix release intended for Docker users, smoothing the experience of TemplateFlow
when using the -u UID
flag is necessary.
FIX: Orientation problem with niworkflows<0.7.2 (nipreps/niworkflows#312) @effigies
ENH: TemplateFlow +
docker run -u ...
(#1525) @oestebanENH: Include repetition time in functional summary (#1508) @wiheto
FIX: Do not crash if all aroma components are classified as noise (#1467) @jdkent
1.3.0.post2 (February 14, 2019)
Hotfix release intended for Singularity users, amending the previous iteration that didn’t fix the problem (#1510) @effigies.
1.3.0.post1 (February 8, 2019)
Hotfix release intended for Singularity users. For further detail, please see #1500.
1.3.0 (February 7, 2019)
We start the 1.3.x series including a few bugfixes, housekeeping duty and a refactors to leverage sMRIPrep (which is a fork of fMRIPrep’s anatomical workflow), pybids>=0.7 for querying dataset, and TemplateFlow for handling standard spaces.
FIX: Bad
fsnative
replacement in CIfTI workflow (#1476) @oestebanFIX: Avoid warning when generating boilerplate (#1464) @oesteban
MAINT: resolves #1485 : patch fmriprep-docker automount for use with Python 3.7 (#1486) @rciric
RF: Use anatomical workflows from sMRIPrep (#1482) @oesteban
MAINT: Update sentry-sdk (#1490) @chrisfilo
ENH: Remaining TemplateFlow integrations (#1494) @oesteban
MAINT: Update to keep up with nipreps/niworkflows#299 (#1496) @oesteban
FIX: Updating bids-validator to 1.1.3 (#1498) @chrisfilo
1.2.x series (January 2019)
1.2.6-1 (January 24, 2019)
Hotfix release of version 1.2.6, pinning niworkflows to a release version (instead of the development branch, since #1459) and including to bugfixes.
PIN: NiWorkflows 0.5.2.post7 (1bf4a21).
FIX: Bad
fsnative
replacement in CIfTI workflow (#1476) @oestebanFIX: Avoid warning when generating boilerplate (#1464) @oesteban
1.2.6 (January 17, 2019)
This is a bug fix release in the 1.2 series. Probably the most noticeable improvement is the restoration of auto-generated content in the documentation.
Additionally, FreeSurfer aparc
/aseg
segmentations are now sampled to all
output spaces.
For any users importing fMRIPrep interfaces, many of these have been moved to the niworkflows package.
With thanks to Nir Jacoby and Hrvoje Stojic for contributions.
FIX: Use keyword arguments for Sentry breadcrumb reporting (#1441) @chrisfilo
FIX: Verify proc file exists before reading (#1454) @effigies
ENH: Only report participants with errors (#1437) @effigies
ENH: Resample aparc/aseg into specified output spaces (#1401) @nirjacoby
ENH: Copy BibTeX file to log directory for LaTeX users (#1446) @hstojic
RF: Use niworkflows upstreamed interfaces and utilities (#1438) @oesteban
DOC: Fix documentation build (#1451) @oesteban
DOC: Fix ReadTheDocs builds (#1459) @effigies
MAINT/DOC: Clean-up
__about__
, update with Nat Meth (#1445) @oestebanMAINT: Make sure Python 3.7.1 is installed (#1452) @oesteban
MAINT: Dev status to beta, bump copyright year (#1468) @effigies
1.2.5 (December 4, 2018)
Hotfix release.
FIX: Breadcrumb reporting (#1435) @chrisfilo
1.2.4 (December 3, 2018)
Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates (with thanks to @emdupre).
ENH: Update ME-EPI workflow to create optimal combination (#1263) @emdupre
MAINT: Merge master into multiecho (#1324) @effigies
ENH: Add echo-idx flag (#1355) @emdupre
FIX: Always run FreeSurfer interfaces that sink outside working directory (#1397) @effigies
ENH: Use Python 3.7 in Dockerfile (#1398) @effigies
DOC: Update contributing guide and add code of conduct (#1404) @emdupre
FIX: Calculate template transforms explicitly as RAS2RAS (#1399) @effigies
MAINT: Replace
img.get_affine()
->img.affine
(#1414) @oestebanFIX: Truncating of sentry messages (#1417) @chrisfilo
ENH: Add fmriprep-docker execution environment (#1416) @chrisfilo
MAINT: Update indexed_gzip to handle small .nii.gz (#1421) @effigies
ENH: Group common issues with fingerprints (#1418) @chrisfilo
ENH: adding memory and cpu info to sentry logs (#1420) @chrisfilo
ENH: Use standard T2* map as coregistration target (#1383) @emdupre
ENH: Handle FreeSurfer subject directory preparation gracefully when run in parallel (#1413) @effigies
ENH: Make sure inputs are BIDS compliant before running fmriprep (#1419) @chrisfilo
ENH: Sentry event categorization propagation (#1422) @chrisfilo
MAINT: Require nipype >= 1.1.6 (#1426) @effigies
ENH: Omnibus multi-echo pull request (#1296) @effigies
ENH: Report memory overcommit policies (#1429) @effigies
1.2.3 (November 16, 2018)
Refactor of Sentry reporting, bug fixes and added tests. With thanks to @sebnaze for contributions.
TST: Utility functions for skipping/re-inserting non-steady-state volumes (#1382) @jdkent
FIX: Correctly populate right-hemisphere time series in CIFTI derivatives (#1378) @sebnaze
FIX: Restore original contour colors in reports (#1385) @oesteban
ENH: New sentry SDK (#1381) @chrisfilo
ENH: Sentry refinement (#1394) @chrisfilo
1.2.2 (November 9, 2018)
Several bug fixes. With thanks to Franz Liem, Nir Jacoby and Markus Handal Sneve for contributions.
FIX: Do not show –debug deprecation warning unless used (#1361) @effigies
FIX: Select consistent parcellation for producing aparcaseg derivatives (#1369) @nirjacoby
FIX: Count non-steady-state volumes even if sbref is passed (#1373) @effigies
ENH: Respect SliceEncodingDirection metadata (#1350) @fliem
ENH: Set maximum MELODIC components to 200 by default (#1366) @markushs
TST: Verify LegacyMultiProc functionality (#1368) @effigies
1.2.1 (November 1, 2018)
Hotfix release (deployment system)
1.2.0 (October 31, 2018)
This release marks a substantial renaming of derivatives to conform to the BIDS Derivatives specification [release candidate](https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI/).
The most significant additional change is a substantial revision of BOLD skull-stripping, using a BOLD template constructed from many open datasets. Building off the work of Zhifang Ye (see #1050), the skull-stripping is now much more resilient to intensity inhomogeneity.
With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhifang Ye for contributions.
FIX: Missing BOLD reports (#1326) @oesteban
FIX: Ensure encoding when reading boilerplate (#1322) @alioco
FIX: Reportlets - bbregister vs flirtbbr (continues #1326) (#1328) @oesteban
FIX: Quick update to new template structure (#1330) @oesteban
FIX: Explicitly pass bold mask to AROMA (#1332) @jdkent
FIX: Missing report output - #1339 (#1346) @kasbohm
FIX: Remove non-steady-state volumes prior to ICA-AROMA (#1335) @jdkent
ENH: Store BOLD reference images (#1306) @oesteban
ENH: Deprecate –debug with –sloppy (#1347) @effigies
ENH: Conform confound regressor names to Derivatives RC2 (#1343) @effigies
ENH: Do not set KEEP_FILE_OPEN_DEFAULT (#1356) @effigies
ENH: Template-based masking of EPI boldrefs (#1321) @oesteban
DOC: Update BIDS-validator link (#1320) @surchs
DOC: add –bind method to singularity patch documentation (#1340) @jdkent
RF: Update anatomical derivatives for RC1 (#1325) @effigies
RF: Update functional derivatives for RC1 (#1333) @effigies
TST: Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
TST: Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
MAINT: Ignore project settings files from popular python/code editors (#1336) @jdkent
CI: Deploy nipreps/fmriprep:unstable tracking master (#1307) @effigies
1.1.x series (October 2018)
1.1.8 (October 4, 2018)
Several bug fixes. This release is intended to be the last before start adopting BIDS-Derivatives RC1 (which will trigger 1.2.x versions).
DOC: Switch to orig graph for
init_bold_t2s_wf
(#1298) @effigiesFIX: Enhance T2 contrast
enhance_t2
in reference estimate (#1299) @effigiesFIX: Create template from one usable T1w image (#1305) @effigies
MAINT: Pin grabbit and pybids in
setup.py
(#1284) @oesteban
1.1.7 (September 25, 2018)
Several bug fixes. With thanks to Elizabeth Dupre and Romain Vala for contributions.
FIX: Revert FreeSurfer download URL (#1280) @chrisfilo
FIX: Default to 6 DoF for BOLD-T1w registration (#1286) @effigies
FIX: Only grab sbref images, not metadata (#1285) @effigies
FIX: QwarpPlusMinus renamed source_file to in_file (#1289) @effigies
FIX: Remove long paths from all LTA output files (#1274) @romainVala
ENH: Use single-band reference images when available (#1270) @effigies
DOC: Note GIFTI surface alignment (#1288) @effigies
RF: Split BOLD-T1w registration into calculation/application workflows (#1278) @emdupre
MAINT: Pin pybids and grabbit in Docker build (#1281) @chrisfilo
1.1.6 (September 10, 2018)
Hotfix release.
FIX: Typo in plugin config loading.
1.1.5 (September 06, 2018)
Improved documentation and minor bug fixes. With thanks to Jarod Roland and Taylor Salo for contributions.
DOC: Replace
--clearenv
with correct--cleanenv
flag (#1237) @jarodrolandDOC: De-indent to remove text from code block (#1238) @effigies
TST: Add enhance-and-skullstrip regression tests (#1074) @effigies
DOC: Clearly indicate that fMRIPrep requires Python 3.5+ (#1249) @oesteban
MAINT: Update PR template (#1239) @effigies
DOC: Set appropriate version in Zenodo citation (#1250) @oesteban
DOC: Updating long description (#1230) @oesteban
DOC: Add ME workflow description (#1253) @tsalo
FIX: Add memory annotation to ROIPlot interface (#1256) @jdkent
ENH: Write derivatives
dataset_description.json
(#1247) @effigiesDOC: Enable table text wrap and link docstrings to code on GitHub (#1258) @tsalo
DOC: Clarify language describing T1w image merging (#1269) @chrisfilo
FIX: Accommodate new template formats (#1273) @effigies
FIX: Permit overriding plugin config with CLI options (#1272) @effigies
1.1.4 (August 06, 2018)
A hotfix release for #1235. Additionally, notebooks have been synced with the latest version of that repository.
FIX: Verify first word of
_cmd
in dependency check (#1236)DOC: Add two missing references (#1234)
ENH: Allow turning off random seeding for ANTs brain extraction (#919)
1.1.3 (July 30, 2018)
This release comes with many updates to the documentation, a more lightweight
SignalExtraction
, a new dynamic boilerplate and some new features from
Nipype.
ENH: Use upstream
afni.TShift
improvements (#1160)PIN: Nipype 1.1.1 (65078c9)
ENH: Dynamic citation boilerplate (#1024)
ENH: Check Command Line dependencies before running (#1044)
ENH: Reimplement
SignalExtraction
(#1170)DOC: Update copyright year to 2018 (#1224)
ENH: Enable
-u
(docker user/userid) flag in wrapper (#1223)FIX: Corrects Dockerfile
WORKDIR
. (#1218)ENH: More specific errors for missing echo times (#1221)
ENH: Change
WORKDIR
of Docker image (#1204)DOC: Update documentation related to contributions (#1187)
DOC: Additions to include before responding to reviews of the pre-print (#1195)
DOC: Improving documentation on using Singularity (#1063)
DOC: Add OHBM 2018 poster, presentation (#1198)
ENH: Replace
InvertT1w
with upstreamRescale(invert=True)
(#1161)
1.1.2 (July 6, 2018)
This release incorporates Nipype improvements that should reduce the chance of hanging if tasks are killed for excessive resource consumption.
Thanks to Elizabeth DuPre for documentation updates.
DOC: Clarify how to reuse FreeSurfer derivatives (#1189)
DOC: Improve command line option documentation (#1186, #1080)
MAINT: Update core dependencies (#1179, #1180)
1.1.1 (June 7, 2018)
ENH: Pre-cache DKT31 template in Docker image (#1159)
MAINT: Update core dependencies (#1163)
1.1.0 (June 4, 2018)
ENH: Use Reorient interface included upstream in nipype (#1153)
FIX: Refine BIDS queries to avoid indexing derivatives (#1141)
DOC: Clarify outlier columns (#1138)
PIN: Update to niworkflows 0.4.0 and nipype 1.0.4 (#1133)
1.0.x series (May 2018)
1.0.15 (May 17, 2018)
DOC: Add lesion masking during registration (#1113)
FIX: Patch
boldbuffer
for ME (#1134)
1.0.14 (May 15, 2018)
With thanks to @ZhifangYe for contributions
FIX: Non-invertible transforms bringing parcellation to BOLD (#1130)
FIX: Bad connection for
--medial-surface-nan
option (#1128)
1.0.13 (May 11, 2018)
With thanks to @danlurie for the outstanding contribution of #1106
ENH: Some nit picks on reports (#1123)
ENH: Carpetplot + confounds plot (#1114)
ENH: Add constrained cost-function masking to T1-MNI registration (#1106)
FIX: Circular dependency (#1104)
ENH: Set
PYTHONNOUSERSITE
in containers (#1103)
1.0.12 (May 03, 2018)
MAINT: fmriprep-docker: Ensure data/output/work paths are absolute (#1089)
ENH: Add usage tracking and centralized error reporting (#1088)
FIX: Ensure one motion IC index is loaded as list (#1096)
TST: Refactoring CircleCI setup (#1098)
FIX: Compression in DataSinks (#1095)
MAINT: fmriprep-docker: Support Python 2/3 without future or other helpers (#1082)
MAINT: Update npm to 10.x (#1087)
DOC: Prefer pre-print over Zenodo doi in boilerplate (#1086)
DOC: Stylistic fix (`’template’`) (#1083)
FIX: Run ICA-AROMA in
MNI152Lin
2mm resampling grid (91x109x91 vox) (#1064)MAINT: Remove cwebp to revert to png (#1081)
ENH: Allow changing the dimensionality of Melodic for AROMA. (#1052)
FIX: Derivatives datasink handling of compression (#1077)
FIX: Check for invalid sform matrices (#1072)
FIX: Check exit code from subprocess (#1073)
DOC: Add preprint fig. 1 to About (#1070)
FIX: Always strip session from T1w for derivative naming (#1071)
DOC: Add RRIDs in the citation boilerplate (#1061)
ENH: Generate CIFTI derivatives (#1001)
1.0.11 (April 16, 2018)
FIX: Do not detrend CSF/WhiteMatter/GlobalSignal (#1058)
1.0.10 (April 16, 2018)
TST: Re-run ds005 with only one BOLD run (#1048)
FIX: Patch subject_summary in reports (#1047)
1.0.9 (April 10, 2018)
With thanks to @danlurie for contributions.
FIX: Connect inputnode to SDC for pepolar images (#1046)
FIX: Pass
ref_file
to STC check (#1038)DOC: Add BBR fallback to user docs. (#1036)
ENH: Revise resampling grid for template outputs (#1040)
MAINT: DataSinks within their workflows (#1021)
ENH: Add FLAIR pial refinement support (#829)
MAINT: Upgrade to pybids 0.5 (#1027)
MAINT: Refactor fieldmap heuristics (#1017)
FIX: Use metadata to select shortest echo as ref_file (#1018)
ENH: Adopt versioneer to compose version names (#1007)
ENH: Handle first echo separately for ME-EPI (#891)
1.0.8 (February 22, 2018)
With thanks to @mgxd and @naveau for contributions.
FIX: ROIs Plot and output brain masks consistency (#1002)
FIX: Init flirt with qform (#1003)
DOC: Prepopulate tag when posting neurostars questions. (#987)
FIX: Update fmap.py : import _get_pe_index in get_ees (#984)
FIX: Argparse action (#985)
1.0.7 (February 13, 2018)
ENH: Output
aseg
andaparc
in T1w and BOLD spaces (#957)FIX: Write latest BOLD mask out (space-T1w) (#978)
PIN: Updating niworkflows to 0.3.1 (#962)
FIX: Robuster BOLD mask (#966)
1.0.6 (29th of January 2018)
FIX: Bad connection in phasediff-fieldmap workflow (#950)
PIN: niworkflows-0.3.1-dev (including Nipype 1.0.0!)
ENH: Migrate to CircleCI 2.0 and workflows (#943)
ENH: Improvements to CLIs (native & wrapper) (#944)
FIX: Rerun tCompCor interface in case of MemoryError (#942)
1.0.5 (21st of January 2018)
PIN: niworkflows-0.2.8 to fix several execution issues.
ENH: Code cleanup (#938)
1.0.4 (15th of January 2018)
FIX: Pin niworkflows-0.2.6 to fix several MultiProc errors (nipy/nipype#2368)
DOC: Fix DOI in citation boilerplate (#933)
FIX: Heuristics to prevent memory errors during aCompCor (#930).
FIX: RuntimeWarning: divide by zero encountered in float_scalars (#931).
FIX: INU correction before merging several T1w (#925).
1.0.3 (3rd of January 2018)
FIX: Pin niworkflows-0.2.4 to fix (#868).
FIX: Roll back run/task groupings after BIDS query (#918). Groupings for the multi-echo extension will be reenabled soon.
1.0.2 (2nd of January 2018)
FIX: Grouping runs broke FMRIPREP on some datasets (#916) Thanks to @emdupre
1.0.1 (1st of January 2018)
With thanks to @emdupre for contributions.
PIN: Update required niworkflows version to 0.2.3
FIX: Refine
antsBrainExtraction
ifrecon-all
is run (#912) With thanks to Arno Klein for his [helpful comments here](https://github.com/nipreps/fmriprep/issues/431#issuecomment-299583391)FIX: Use thinner contours in reportlets (#910)
FIX: Robuster EPI mask (#911)
FIX: Set workflow return value before potential error (#887)
DOC: Documentation about FreeSurfer and
--fs-no-reconall
(#894)DOC: Fix example in installation ants-nthreads -> omp-nthreads (#885) With thanks to @mvdoc.
ENH: Allow for multiecho data (#875)
1.0.0 (6th of December 2017)
ENH: Add
--resource-monitor
flag (#883)FIX: Collision between Multi-T1w and
--no-freesurfer
(#880)FIX: Setting
use_compression
on resampling workflows (#882)ENH: Estimate motion parameters before STC (#876)
ENH: Add
--stop-on-first-crash
option (#865)FIX: Correctly handling xforms (#874)
FIX: Combined ROI reportlets (#872)
ENH: Strip reportlets out of full report (#867)
1.0.0-rc13 (1st of December 2017)
FIX: Broken
--fs-license-file
argument (#869)
1.0.0-rc12 (29th of November 2017)
ENH: Use Nipype MultiProc even for sequential execution (#856)
RF: More memory annotations and considerations (#816)
FIX: Controlling memory explosion (#854)
FIX: Mount nipype repositories as niworkflows submodule (#834)
FIX: Reduce image loads in local memory (#839)
ENH: Always sync qforms, refactor error messaging (#851)
1.0.0-rc11 (24th of November 2017)
ENH: Check for invalid qforms in validation (#847)
FIX: Update pybids to include latest bugfixes (#838)
FIX: MultiApplyTransforms failed with nthreads=1 (#835)
1.0.0-rc10 (9th of November 2017)
FIX: Adopt new FreeSurfer (v6.0.1) license mechanism (#787)
ENH: Output affine transforms from original T1w images to preprocessed anatomical (#726)
FIX: Correct headers in AFNI-generated NIfTI files (#818)
FIX: Normalize T1w image qform/sform matrices (#820)
1.0.0-rc9 (2nd of November 2017)
FIX: Fixed #776 (aCompCor - numpy.linalg.linalg.LinAlgError: SVD did not converge) via #807.
ENH: Added
CSF
column to_confounds.tsv
(included in #807)DOC: Add more details on the outputs of FMRIPREP and minor fixes (#811)
ENH: Processing confounds in BOLD space (#807)
ENH: Updated niworkflows and nipype, including the new feature to close all file descriptors (#810)
RF: Refactored BOLD workflows module (#805)
ENH: Improved memory annotations (#803, #807)
1.0.0-rc8 (27th of October 2017)
FIX: Allow missing magnitude2 in phasediff-type fieldmaps (#802)
FIX: Lower tolerance deciding t1_merge shapes (#798)
FIX: Be robust to 4D T1w images (#797)
ENH: Resource annotations (#746)
ENH: Use indexed_gzip with nibabel (#788)
FIX: Reduce FoV of outputs in T1w space (#785)
1.0.0-rc7 (20th of October 2017)
ENH: Update pinned version of nipype to latest master
ENH: Added rX permissions to make life easier on Singularity users (#757)
DOC: Citation boilerplate (#779)
FIX: Patch to remove long filenames after mri_concatenate_lta (#778)
FIX: Only use unbiased template with
--longitudinal
(#771)FIX: Use t1_2_fsnative registration when sampling to surface (#762)
ENH: Remove
--skull_strip_ants
option (#761)DOC: Add reference to beginners guide (#763)
1.0.0-rc6 (11th of October 2017)
ENH: Add inverse normalization transform (MNI -> T1w) to derivatives (#754)
ENH: Fall back to initial registration if BBR fails (#694)
FIX: Header and affine transform updates to resolve intermittent misalignments in reports (#743)
FIX: Register FreeSurfer template to FMRIPREP template, handling pre-run FreeSurfer subjects more robustly, saving affine to derivatives (#733)
ENH: Add OpenFMRI participant sampler command-line tool (#704)
ENH: For SyN-SDC, assume phase-encoding direction of A-P unless specified L-R (#740, #744)
ENH: Permit skull-stripping with NKI ANTs template (#729)
ENH: Erode aCompCor masks to target volume proportions, instead of fixed distances (#731, #732)
DOC: Documentation updates (#748)
1.0.0-rc5 (25th of September 2017)
FIX: Skip slice time correction on BOLD series < 5 volumes (#711)
FIX: Skip AFNI check for new versions (#723)
DOC: Documentation clarification and updates (#698, #711)
1.0.0-rc4 (12th of September 2017)
With thanks to Mathias Goncalves for contributions.
ENH: Collapse ITK transforms of head-motion correction in only one file (#695)
FIX: Raise error when run.py is called directly (#692)
FIX: Parse crash files when they are stored as text (#690)
ENH: Replace medial wall values with NaNs (#687)
1.0.0-rc3 (28th of August 2017)
With thanks to Anibal Sólon for contributions.
ENH: Add
--low-mem
option to reduce memory usage for large BOLD series (#663)ENH: Parallelize anatomical conformation step (#666)
FIX: Handle missing functional data in SubjectSummary node (#670)
FIX: Disable
--no-skull-strip-ants
(AFNI skull-stripping) (#674)FIX: Initialize SyN SDC more robustly (#680)
DOC: Add comprehensive documentation of workflow API (#638)
1.0.0-rc2 (12th of August 2017)
ENH: Increased support for partial field-of-view BOLD datasets (#659)
FIX: Slice time correction is now being applied to output data (not only to intermediate file used for motion estimation - #662)
FIX: Fieldmap unwarping is now being applied to MNI space outputs (not only to T1w space outputs - #662)
1.0.0-rc1 (8th of August 2017)
ENH: Include ICA-AROMA confounds in report (#646)
ENH: Save non-aggressively denoised BOLD series (#648)
ENH: Improved logging messages (#621)
ENH: Improved resource management (#622, #629, #640, #641)
ENH: Improved confound header names (#634)
FIX: Ensure multi-T1w image datasets have RAS-oriented template (#637)
FIX: More informative errors for conflicting options (#632)
DOC: Improved report summaries (#647)
0.x series (July 2017)
0.6.0 (31st of July 2017)
With thanks to Yaroslav Halchenko and Ilkay Isik for contributions.
ENH: Set threshold on up-sampling ratio in conformation, report results (#601)
ENH: Censor non-steady-state volumes prior to CompCor (#603)
FIX: Conformation failure in thick-slice, oblique T1w datasets (#601)
FIX: Crash/report failure of phase-difference SDC pipeline (#602, #604)
FIX: Prevent AFNI NIfTI extensions from crashing reference EPI estimation (#619)
DOC: Save logs to output directory (#605)
ENH: Upgrade to ICA-AROMA 0.4.1-beta (#611)
0.5.4 (20th of July 2017)
DOC: Improved report summaries describing steps taken (#584)
ENH: Uniformize command-line argument style (#592)
0.5.3 (18th of July 2017)
With thanks to Yaroslav Halchenko for contributions.
ENH: High-pass filter time series prior to CompCor (#577)
ENH: Validate and minimally conform BOLD images (#581)
FIX: Bug that prevented PE direction estimation (#586)
DOC: Log version/time in report (#587)
0.5.2 (30th of June 2017)
With thanks to James Kent for contributions.
ENH: Calculate noise components in functional data with ICA-AROMA (#539)
FIX: Remove unused parameters from function node, resolving crash (#576)
0.5.1 (24th of June 2017)
FIX: Invalid parameter in
bbreg_wf
(#572)
0.5.0 (21st of June 2017)
With thanks to James Kent for contributions.
ENH: EXPERIMENTAL: Fieldmap-less susceptibility correction with
--use-syn-sdc
option (#544)FIX: Reduce interpolation artifacts in ConformSeries (#564)
FIX: Improve consistency of handling of fieldmaps (#565)
FIX: Apply T2w pial surface refinement at correct stage of FreeSurfer pipeline (#568)
ENH: Add
--anat-only
workflow option (#560)FIX: Output all tissue class/probability maps (#569)
ENH: Upgrade to ANTs 2.2.0 (#561)
0.4.6 (14th of June 2017)
ENH: Conform and minimally resample multiple T1w images (#545)
FIX: Return non-zero exit code on all errors (#554)
ENH: Improve error reporting for missing subjects (#558)
0.4.5 (12th of June 2017)
With thanks to Marcel Falkiewicz for contributions.
FIX: Correctly display help in
fmriprep-docker
(#533)FIX: Avoid invalid symlinks when running FreeSurfer (#536)
ENH: Improve dependency management for users unable to use Docker/Singularity containers (#549)
FIX: Return correct exit code when a Function node fails (#554)
0.4.4 (20th of May 2017)
With thanks to Feilong Ma for contributions.
ENH: Option to provide a custom reference grid image (
--output-grid-reference
) for determining the field of view and resolution of output images (#480)ENH: Improved EPI skull stripping and tissue contrast enhancements (#519)
ENH: Improve resource use estimates in FreeSurfer workflow (#506)
ENH: Moved missing values in the DVARS* and FramewiseDisplacement columns of the _confounds.tsv from last row to the first row (#523)
ENH: More robust initialization of the normalization procedure (#529)
0.4.3 (10th of May 2017)
ENH:
--output-space template
targets template specified by--template
flag (MNI152NLin2009cAsym
supported) (#498)FIX: Fix a bug causing small numerical discrepancies in input data voxel size to lead to different FOV of the output files (#513)
0.4.2 (3rd of May 2017)
ENH: Use robust template generation for multiple T1w images (#481)
ENH: Anatomical MNI outputs respect
--output-space
selection (#490)ENH: Added support for distortion correction using opposite phase encoding direction EPI images (#493)
ENH: Switched to FSL BET for skullstripping of EPI images (#493)
ENH:
--omp-nthreads
controls maximum per-process thread count; replaces--ants-nthreads
(#500)
0.4.1 (20th of April 2017)
Hotfix release (dependencies and deployment system)
0.4.0 (20th of April 2017)
ENH: Added an option to choose the degrees of freedom used when doing BOLD to T1w coregistration (
--bold2t1w_dof
). Set default to 9 to account for field inhomogeneities and coils heating up (#448)ENH: Added support for phase difference and GE style fieldmaps (#448)
ENH: Generate GrayWhite, Pial, MidThickness and inflated surfaces (#398)
ENH: Memory and performance improvements for calculating the EPI reference (#436)
ENH: Sample functional series to subject and
fsaverage
surfaces (#391)ENH: Output spaces for functional data may be selected with
--output-space
option (#447)ENH:
--skip-native
functionality replaced by--output-space
(#447)ENH:
fmriprep-docker
wrapper script simplifies running in a Docker environment (#317)
0.3.2 (7th of April 2017)
With thanks to Asier Erramuzpe for contributions.
ENH: Added optional slice time correction (#415)
ENH: Removed redundant motion parameter conversion step using avscale (#415)
ENH: FreeSurfer submillimeter reconstruction may be disabled with
--no-submm-recon
(#422)ENH: Switch bbregister init from
fsl
tocoreg
(FreeSurfer native #423)ENH: Motion estimation now uses a smart reference image that takes advantage of T1 saturation (#421)
FIX: Fix report generation with
--reports-only
(#427)
0.3.1 (24th of March 2017)
ENH: Perform bias field correction of EPI images prior to coregistration (#409)
FIX: Fix an orientation issue affecting some datasets when bbregister was used (#408)
ENH: Minor improvements to the reports aesthetics (#428)
0.3.0 (20th of March 2017)
FIX: Affine and warp MNI transforms are now applied in the correct order
ENH: Added preliminary support for reconstruction of cortical surfaces using FreeSurfer
ENH: Switched to bbregister for BOLD to T1 coregistration
ENH: Switched to sinc interpolation of preprocessed BOLD and T1w outputs
ENH: Preprocessed BOLD volumes are now saved in the T1w space instead of mean BOLD
FIX: Fixed a bug with MCFLIRT interpolation inducing slow drift
ENH: All files are now saved in Float32 instead of Float64 to save space
0.2.0 (13th of January 2017)
Initial public release
0.1.2 (3rd of October 2016)
FIX: Downloads from OSF, remove data downloader (now in niworkflows)
FIX: pybids was missing in the install_requires
FIX: Deprecated
-S
/--subject-id
tagENH: Accept subjects with several T1w images (#114)
ENH: Documentation updates (#130, #131)
TST: Re-enabled CircleCI tests on one subject from ds054 of OpenfMRI
ENH: Add C3D to docker image, updated poldracklab hub (#128, #119)
ENH: CLI is now BIDS-Apps compliant (#123)
0.1.1 (30th of July 2016)
ENH: Grabbit integration (#113)
ENH: More outputs in MNI space (#99)
ENH: Implementation of phase-difference fieldmap estimation (#91)
ENH: Fixed bug using non-RAS EPI
ENH: Works on ds005 (datasets without fieldmap nor sbref)
ENH: Outputs start to follow BIDS-derivatives (WIP)
0.0.1
ENH: Added Docker images
DOC: Added base code for automatic publication to RTD.
Set up CircleCI with a first smoke test on one subject.
BIDS tree scrubbing and subject-session-run selection.
Refactored big workflow into consistent pieces.
Migrated Craig’s original code