ENH: Restore CIFTI-2 generation #3129
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
effigies
force-pushed
the
enh/restore-cifti-take-2
branch
3 times, most recently
from
7baefba to
0d1be7a
Compare
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## next #3129 +/- ##
==========================================
+ Coverage 48.20% 48.22% +0.01%
==========================================
Files 53 53
Lines 4134 4131 -3
==========================================
- Hits 1993 1992 -1
+ Misses 2141 2139 -2
☔ View full report in Codecov by Sentry. |
Merged
|
This is ready for review. Will move onto carpetplots building on this. |
effigies
force-pushed
the
enh/restore-cifti-take-2
branch
from
19e9022 to
da91be4
Compare
effigies
force-pushed
the
enh/restore-cifti-take-2
branch
from
da91be4 to
21b79e7
Compare
|
Tests passing. @mgxd do you have time to review? |
mgxd
approved these changes
Nov 13, 2023
| suffix='bold', | ||
| compress=False, | ||
| TaskName=all_metadata[0].get('TaskName'), | ||
| **prepare_timing_parameters(all_metadata[0]), |
There was a problem hiding this comment.
not necessarily related to this PR, but is this the only time we are outputing this metadata? seems like something we should only calculate once and then distribute to any bold outputs
There was a problem hiding this comment.
No, we also calculate it in the volumetric workflow:
fmriprep/fmriprep/workflows/bold/outputs.py
Lines 686 to 737 in c294028
So it gets recalculated several times. We could refactor the function to have a cacheable core (can't @lru_cache with a dictionary argument), but I'm not sure saving <1s (estimate, not measured) at workflow build is really worth it.
effigies
added a commit
that referenced
this pull request
Jan 10, 2024
23.2.0 (January 10, 2024) New feature release in the 23.2.x series. This release wraps up a significant refactor of fMRIPrep. The main new features can be used with the ``--level`` and ``--derivatives`` flags. The ``--level`` flag can take the arguments ``minimal``, ``resampling`` or ``full``. The default is ``full``, which should produce nearly the same results as previous versions. ``minimal`` will produce only the minimum necessary to deterministically generate the remaining derivatives. ``resampling`` will produce some additional derivatives, intended to simplify resampling with other tools. The ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``, for example ``--derivatives anat=$SMRIPREP_DIR``. If provided, fMRIPrep will read the specified directories for pre-computed derivatives. If a derivative is found, it will be used instead of computing it from scratch. If a derivative is not found, fMRIPrep will compute it and proceed as usual. Taken together, these features can allow a dataset provider to run a minimal fMRIPrep run, targeting many output spaces, while a user can then run a ``--derivatives`` run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default fMRIPrep behavior, enabling easier workarounds for bugs or experimentation with alternatives. Additionally, this release includes a number of bug fixes and improvements. This release adds support for MSM-Sulc, improving the alignment of subject surfaces to the fsLR template. This process is enabled by default, but may be disabled with the ``--no-msm`` flag. This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity. To disable Jacobian weighting, use ``--ignore fmap-jacobian``. Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future. * FIX: Restore --ignore sbref functionality (#3180) * FIX: Retrieve atlas ROIs at requested density (#3179) * FIX: Keep minctracc executable in FreeSurfer installation (#3175) * FIX: Exclude echo entity from optimally combined derivatives (#3166) * FIX: Disable boldref-space outputs unless requested (#3159) * FIX: Tag memory estimates in resamplers (#3150) * FIX: Final revisions for next branch (#3134) * FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (#3098) * FIX: Connect EPI-to-fieldmap transform (#3099) * FIX: Use Py2-compatible version file template for fmriprep-docker (#3101) * FIX: Update connections to unwarp_wf, convert ITK transforms to text (#3077) * ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction (#3186) * ENH: Exclude non-steady-state volumes from confound correlation plot (#3171) * ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate (#3146) * ENH: Restore carpetplot and other final adjustments (#3131) * ENH: Restore CIFTI-2 generation (#3129) * ENH: Restore resampling to surface GIFTIs (#3126) * ENH: Restore confound generation (#3120) * ENH: Restore resampling BOLD to volumetric templates (#3121) * ENH: Restore resampling to T1w target (#3116) * ENH: Add MSMSulc (#3085) * ENH: Add reporting workflow for BOLD fit (#3082) * ENH: Generate anatomical derivatives useful for resampling (#3081) * RF: Load reportlets interfaces from nireports rather than niworkflows (#3176, #3184) * RF: Separate goodvoxels mask creation from fsLR resampling (#3170) * RF: Write out anatomical template derivatives (#3136) * RF: Update primary bold workflow to incorporate single shot resampling (#3114) * RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (#3078) * RF: Split fMRIPrep into fit and derivatives workflows (#2913) * RPT: Rename CSF/WM confounds in fMRIPlot (#3172) * TST: Add smoke tests for full workflow and most branching flags (#3155) * TST: Add smoke-tests for bold_fit_wf (#3152) * DOC: Fix documentation and description for init_bold_grayords_wf (#3051) * DOC: Minor updates in outputs.rst (#3148) * STY: Apply a couple refurb suggestions (#3151) * STY: Fix flake8 warnings (#3044) * STY: Apply pyupgrade suggestions (#3043) * MNT: Restore mritotal subcommands to Dockerfile (#3149) * MNT: Update smriprep to 0.13.1 (#3153) * MNT: optimise size of PNG files (#3145) * MNT: update vendored docs script ``github_link.py`` (#3144) * MNT: Update tedana pin, test on Python 3.12 (#3141) * MNT: Bump environment (#3132) * MNT: Bump version requirements (#3107) * MNT: http:// → https:// (#3097) * MNT: Remove mritotal and dependencies from FreeSurfer ignore file (#3090) * MNT: Update environment (#3073) * MNT: Depend on newer sphinx (#3067) * MNT: Install ANTs from conda-forge (#3061) * MNT: Drop Python 3.8 and numpy 1.21 support (NEP29) (#3052) * MNT: update update_zenodo.py script (#3042) * MNT: Fix welcome message formatting and instructions (#3039) * MNT: Python 3.11 should be supported (#3038) * CI: Bump actions/setup-python from 4 to 5 (#3181) * CI: Stop testing legacy layout (#3079) * CI: Improve tag detection for docker builds (#3066) * CI: Clean up pre-release builds (#3040)
NingAnMe
added a commit
to NingAnMe/fmriprep
that referenced
this pull request
Jan 11, 2024
23.2.0 (January 10, 2024) New feature release in the 23.2.x series. This release wraps up a significant refactor of fMRIPrep. The main new features can be used with the ``--level`` and ``--derivatives`` flags. The ``--level`` flag can take the arguments ``minimal``, ``resampling`` or ``full``. The default is ``full``, which should produce nearly the same results as previous versions. ``minimal`` will produce only the minimum necessary to deterministically generate the remaining derivatives. ``resampling`` will produce some additional derivatives, intended to simplify resampling with other tools. The ``--derivatives`` flag takes arguments of the form ``name=/path/to/dir``, for example ``--derivatives anat=$SMRIPREP_DIR``. If provided, fMRIPrep will read the specified directories for pre-computed derivatives. If a derivative is found, it will be used instead of computing it from scratch. If a derivative is not found, fMRIPrep will compute it and proceed as usual. Taken together, these features can allow a dataset provider to run a minimal fMRIPrep run, targeting many output spaces, while a user can then run a ``--derivatives`` run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default fMRIPrep behavior, enabling easier workarounds for bugs or experimentation with alternatives. Additionally, this release includes a number of bug fixes and improvements. This release adds support for MSM-Sulc, improving the alignment of subject surfaces to the fsLR template. This process is enabled by default, but may be disabled with the ``--no-msm`` flag. This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity. To disable Jacobian weighting, use ``--ignore fmap-jacobian``. Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future. * FIX: Restore --ignore sbref functionality (nipreps#3180) * FIX: Retrieve atlas ROIs at requested density (nipreps#3179) * FIX: Keep minctracc executable in FreeSurfer installation (nipreps#3175) * FIX: Exclude echo entity from optimally combined derivatives (nipreps#3166) * FIX: Disable boldref-space outputs unless requested (nipreps#3159) * FIX: Tag memory estimates in resamplers (nipreps#3150) * FIX: Final revisions for next branch (nipreps#3134) * FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (nipreps#3098) * FIX: Connect EPI-to-fieldmap transform (nipreps#3099) * FIX: Use Py2-compatible version file template for fmriprep-docker (nipreps#3101) * FIX: Update connections to unwarp_wf, convert ITK transforms to text (nipreps#3077) * ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction (nipreps#3186) * ENH: Exclude non-steady-state volumes from confound correlation plot (nipreps#3171) * ENH: Pass FLAIR images to anatomical workflow builder to include in boilerplate (nipreps#3146) * ENH: Restore carpetplot and other final adjustments (nipreps#3131) * ENH: Restore CIFTI-2 generation (nipreps#3129) * ENH: Restore resampling to surface GIFTIs (nipreps#3126) * ENH: Restore confound generation (nipreps#3120) * ENH: Restore resampling BOLD to volumetric templates (nipreps#3121) * ENH: Restore resampling to T1w target (nipreps#3116) * ENH: Add MSMSulc (nipreps#3085) * ENH: Add reporting workflow for BOLD fit (nipreps#3082) * ENH: Generate anatomical derivatives useful for resampling (nipreps#3081) * RF: Load reportlets interfaces from nireports rather than niworkflows (nipreps#3176, nipreps#3184) * RF: Separate goodvoxels mask creation from fsLR resampling (nipreps#3170) * RF: Write out anatomical template derivatives (nipreps#3136) * RF: Update primary bold workflow to incorporate single shot resampling (nipreps#3114) * RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (nipreps#3078) * RF: Split fMRIPrep into fit and derivatives workflows (nipreps#2913) * RPT: Rename CSF/WM confounds in fMRIPlot (nipreps#3172) * TST: Add smoke tests for full workflow and most branching flags (nipreps#3155) * TST: Add smoke-tests for bold_fit_wf (nipreps#3152) * DOC: Fix documentation and description for init_bold_grayords_wf (nipreps#3051) * DOC: Minor updates in outputs.rst (nipreps#3148) * STY: Apply a couple refurb suggestions (nipreps#3151) * STY: Fix flake8 warnings (nipreps#3044) * STY: Apply pyupgrade suggestions (nipreps#3043) * MNT: Restore mritotal subcommands to Dockerfile (nipreps#3149) * MNT: Update smriprep to 0.13.1 (nipreps#3153) * MNT: optimise size of PNG files (nipreps#3145) * MNT: update vendored docs script ``github_link.py`` (nipreps#3144) * MNT: Update tedana pin, test on Python 3.12 (nipreps#3141) * MNT: Bump environment (nipreps#3132) * MNT: Bump version requirements (nipreps#3107) * MNT: http:// → https:// (nipreps#3097) * MNT: Remove mritotal and dependencies from FreeSurfer ignore file (nipreps#3090) * MNT: Update environment (nipreps#3073) * MNT: Depend on newer sphinx (nipreps#3067) * MNT: Install ANTs from conda-forge (nipreps#3061) * MNT: Drop Python 3.8 and numpy 1.21 support (NEP29) (nipreps#3052) * MNT: update update_zenodo.py script (nipreps#3042) * MNT: Fix welcome message formatting and instructions (nipreps#3039) * MNT: Python 3.11 should be supported (nipreps#3038) * CI: Bump actions/setup-python from 4 to 5 (nipreps#3181) * CI: Stop testing legacy layout (nipreps#3079) * CI: Improve tag detection for docker builds (nipreps#3066) * CI: Clean up pre-release builds (nipreps#3040)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Builds on #3126.
This one splits out the selection of the MNI template for the CIFTI-2 generation from the rest of the resampling to volumetric templates. If someone requests MNI152NLin6Asym and CIFTI, then we will resample twice in the working directory, but given that resampling is significantly faster now and does not scale files per-time point, I'm okay with that. I think it's a pretty rare case, and I suspect we'll want to resample a smaller ROI than the full brain at some point, so a separate pathway for that seems okay.