Issues

• Allow skipping surface reconstruction when all surface derivatives are precomputed

  enhancement
  nipreps/smriprep#584 · Filter by author ChristianGaser opened on Sep 2, 2026
  1

• Difference in INU behavior when providing precomputed mask

  bug
  nipreps/smriprep#574 · Filter by author psadil opened on Jul 28, 2026

• TypeError: 'Namespace' object does not support item assignment when using --longitudinal or --subject-anatomical-reference unbiased

  bug
  nipreps/smriprep#573 · Filter by author joshita89 opened on Jul 3, 2026
  1

• ENH: Upstream BIDSSourceFile and CreateFreeSurferID interfaces from fMRIPrep

  upstream-AnyPrep
  nipreps/smriprep#544 · Filter by author oesteban opened on Feb 15, 2026

• New flag --fs-from-mask-edits

  enhancement
  nipreps/smriprep#539 · Filter by author joey-scanga opened on Feb 12, 2026

• Copy custom templates to sourcedata directory

  BIDSenhancement
  nipreps/smriprep#514 · Filter by author tsalo opened on Dec 5, 2025

• Hanging on fsnative2t1w_xfm

  bug
  nipreps/smriprep#506 · Filter by author joey-scanga opened on Nov 10, 2025
  5

• Invalid argument --regoption passed to MSM

  bug
  nipreps/smriprep#502 · Filter by author oesteban opened on Oct 17, 2025
  4

• Upstream fips_enabled() from fMRIPrep

  upstream-AnyPrep
  nipreps/smriprep#501 · Filter by author oesteban opened on Oct 14, 2025

• mris_expand is slow when using high thread count

  bug
  nipreps/smriprep#490 · Filter by author chrisadamsonmcri opened on May 6, 2025
  6

• Write down the outputs of bias field correction necessary to reconstruct preprocessed T1w data

  enhancement
  nipreps/smriprep#470 · Filter by author celprov opened on Apr 15, 2025

• Myelin maps (T1w/T2w)

  enhancement
  nipreps/smriprep#432 · Filter by author effigies opened on Apr 25, 2024
  3

• Brain tissue segmentation fmriprep wrong labelling for few subjects

  bug
  nipreps/smriprep#431 · Filter by author emvdmeijden opened on Apr 23, 2024

• Any smriprep fix for Freesurfer 7.3.2 FLAIR Pial Surface placement bug?

  freesurfer
  nipreps/smriprep#414 · Filter by author nordicpioneer opened on Feb 15, 2024
  3

• Support newMSM

  enhancement
  nipreps/smriprep#413 · Filter by author effigies opened on Feb 9, 2024

• 23.2.0a3: template_iterator_wf.select_xfm failing with MNIPediatricAsym when cohort specified

  bug
  nipreps/smriprep#407 · Filter by author smeisler opened on Dec 15, 2023
  15

• Denoise and INU correct anatomical images post-merge

  enhancement
  nipreps/smriprep#400 · Filter by author effigies opened on Nov 23, 2023
  1

• Enable longitudinal structural analysis

  effort:mediumfreesurferimpact:high
  nipreps/smriprep#429 · Filter by author ChristianNSchmitz opened on Nov 15, 2023
  13

• singularity issue, growing containers and the like

  enhancement
  nipreps/smriprep#367 · Filter by author hjbockholt opened on Sep 27, 2023
  2

• Add option to use SynthSeg as alternative to recon-all

  enhancement
  nipreps/smriprep#343 · Filter by author tsalo opened on Jun 1, 2023
  5

• Replace hardcoded t1w with anat for multi-modality workflows / nodes

  effort:mediumimpact:lowmaintenance
  nipreps/smriprep#320 · Filter by author mgxd opened on Jan 26, 2023
  1

• --output-layout bids as default for 0.10.x series

  enhancement
  nipreps/smriprep#318 · Filter by author effigies opened on Jan 18, 2023

• Improve documentation on longitudinal option.

  documentation
  nipreps/smriprep#306 · Filter by author bpinsard opened on Oct 18, 2022
  1

• Integrate SynthStrip?

  enhancement
  nipreps/smriprep#299 · Filter by author oesteban opened on Aug 26, 2022
  8

• FreeSurfer execution when both T2w and FLAIR present

  nipreps/smriprep#297 · Filter by author Lestropie opened on Jul 11, 2022 · 0.10.x
  4