1.0.0-rc9

This release is focused on reorganizing the modules of the BOLD processing. Also, the workflow that computes the confound has been refactored and now works in native BOLD space. This new feature is expected to help integrate the --func-only feature (#808), helps keeping memory low (as the input files are a lot smaller) and is more robust to partial-FoV scans.

Also, includes large improvements to the documentation.

CHANGES

• [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)
• [REF] Refactored BOLD workflows module (#805)
• [ENH] Improved memory annotations (#803, #807)

1.0.0-rc8

CHANGES

• [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

• [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

• [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

• [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

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

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

• [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

• [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)

0.6.0

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)