nipreps/fmriprep issues and pull requests

#3312 - DOC: Add benchmark page

Pull Request - State: closed - Opened by effigies 17 days ago - 1 comment

#3311 - Add optional Multiband Artifact Regression in Simultaneous Slices (MARSS) step

Issue - State: open - Opened by tsalo 17 days ago
Labels: feature

#3311 - Add optional Multiband Artifact Regression in Simultaneous Slices (MARSS) step

Issue - State: open - Opened by tsalo 17 days ago
Labels: feature

#3310 - Bump scikit-learn from 1.4.2 to 1.5.0

Pull Request - State: open - Opened by dependabot[bot] 17 days ago
Labels: dependencies, python

#3308 - Add optional NORDIC denoising step

Issue - State: open - Opened by tsalo 18 days ago - 3 comments
Labels: feature

#3308 - Add optional NORDIC denoising step

Issue - State: open - Opened by tsalo 18 days ago - 3 comments
Labels: feature

#3307 - nipype.workflow CRITICAL: fMRIPrep failed: [Errno 13] Permission denied

Issue - State: closed - Opened by CogBrainHealthLab 18 days ago - 5 comments
Labels: bug

#3306 - Prerun freesurfer with -hires and -expert flags are not able to be used with fmriprep

Issue - State: open - Opened by adam-coates 20 days ago - 1 comment
Labels: bug

#3306 - Prerun freesurfer with -hires and -expert flags are not able to be used with fmriprep

Issue - State: open - Opened by adam-coates 20 days ago - 1 comment
Labels: bug

#3305 - Failed to generate the boilerplate

Issue - State: open - Opened by LueHa 21 days ago - 1 comment
Labels: bug

#3305 - Failed to generate the boilerplate

Issue - State: open - Opened by LueHa 21 days ago - 1 comment
Labels: bug

#3304 - Bump tornado from 6.4 to 6.4.1

Pull Request - State: closed - Opened by dependabot[bot] 29 days ago - 1 comment
Labels: dependencies, python

#3303 - msm options no longer work in FSL 6.0.7.11

Issue - State: closed - Opened by CogBrainHealthLab 29 days ago - 2 comments
Labels: bug

#3302 - ENH: Add appropriate titles to HTML reports

Pull Request - State: closed - Opened by effigies 30 days ago - 1 comment

#3301 - REL: 24.0.0

Pull Request - State: closed - Opened by effigies 30 days ago - 1 comment

#3300 - RF: Fix ITK warp conversion to nitransforms format

Pull Request - State: closed - Opened by effigies 30 days ago - 6 comments

#3299 - Crash at workflow build time if total readout time cannot be determined

Issue - State: open - Opened by effigies about 1 month ago

#3299 - Crash at workflow build time if total readout time cannot be determined

Issue - State: open - Opened by effigies about 1 month ago

#3298 - MNT: Pin libitk 5.3 and note dependencies

Pull Request - State: closed - Opened by effigies about 1 month ago - 1 comment

#3297 - Use BIDSURI in init_ds_boldmask_wf

Pull Request - State: closed - Opened by tsalo about 1 month ago - 1 comment
Labels: bug

#3296 - FIX: Ensure shape matches template during resampling

Pull Request - State: closed - Opened by mgxd about 1 month ago - 1 comment

#3295 - numpy.linalg.linalg.LinAlgError: SVD did not converge

Issue - State: open - Opened by begumbabur about 1 month ago
Labels: bug

#3294 - Failure in FMAP and

Issue - State: open - Opened by ikarmann about 1 month ago
Labels: bug

#3293 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago - 1 comment
Labels: dependencies, python

#3293 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: open - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, python

#3292 - FIX: Write out boldref-space brain mask with minimal level

Pull Request - State: closed - Opened by tsalo about 2 months ago - 2 comments
Labels: bug

#3291 - FIX: Write out boldref-space brain mask with minimal level

Pull Request - State: closed - Opened by tsalo about 2 months ago - 1 comment
Labels: bug

#3290 - boldref-space brain mask appears to be missing from minimal outputs

Issue - State: closed - Opened by tsalo about 2 months ago - 2 comments
Labels: bug

#3289 - subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmp3_xycsud.json']' died with <Signals.SIGABRT: 6>.

Issue - State: closed - Opened by m9080212 about 2 months ago - 1 comment
Labels: bug

#3289 - subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmp3_xycsud.json']' died with <Signals.SIGABRT: 6>.

Issue - State: closed - Opened by m9080212 about 2 months ago - 1 comment
Labels: bug

#3288 - Numerical stability testing within series patch releases

Issue - State: open - Opened by mgxd about 2 months ago - 1 comment
Labels: CI, potential hackathon project

#3288 - Numerical stability testing within series patch releases

Issue - State: open - Opened by mgxd about 2 months ago
Labels: CI, potential hackathon project

#3287 - [FIX] Add "double" type to allowed DisplacementFieldTransform

Pull Request - State: closed - Opened by kjamison about 2 months ago - 2 comments

#3287 - [FIX] Add "double" type to allowed DisplacementFieldTransform

Pull Request - State: closed - Opened by kjamison about 2 months ago - 2 comments

#3286 - Consistently getting wrong registration in the same dataset

Issue - State: open - Opened by lalalavi about 2 months ago
Labels: bug

#3286 - Consistently getting wrong registration in the same dataset

Issue - State: open - Opened by lalalavi about 2 months ago
Labels: bug

#3285 - Despite many sessions for a single subject, the reports did not get separated per session

Issue - State: closed - Opened by celprov about 2 months ago - 4 comments
Labels: bug

#3285 - Despite many sessions for a single subject, the reports did not get separated per session

Issue - State: open - Opened by celprov about 2 months ago - 3 comments
Labels: bug

#3283 - MNT: Upgrade ruff pre-commit, add fixing checks

Pull Request - State: closed - Opened by effigies about 2 months ago - 3 comments

#3283 - MNT: Upgrade ruff pre-commit, add fixing checks

Pull Request - State: closed - Opened by effigies about 2 months ago - 3 comments

#3282 - Crash when using --cifti-output

Issue - State: closed - Opened by kjamison about 2 months ago - 3 comments
Labels: bug

#3281 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: open - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, python

#3280 - STY: Apply ruff/pyupgrade rule UP031

Pull Request - State: closed - Opened by DimitriPapadopoulos 2 months ago - 4 comments

#3280 - STY: Apply ruff/pyupgrade rule UP031

Pull Request - State: closed - Opened by DimitriPapadopoulos 2 months ago - 4 comments

#3279 - MNT: complete transition from flake8/black to ruff

Pull Request - State: open - Opened by DimitriPapadopoulos 2 months ago - 2 comments

#3279 - MNT: complete transition from flake8/black to ruff

Pull Request - State: closed - Opened by DimitriPapadopoulos 2 months ago - 2 comments

#3278 - Bump tqdm from 4.66.1 to 4.66.3

Pull Request - State: open - Opened by dependabot[bot] 2 months ago
Labels: dependencies, python

#3278 - Bump tqdm from 4.66.1 to 4.66.3

Pull Request - State: open - Opened by dependabot[bot] 2 months ago
Labels: dependencies, python

#3277 - Randomly fail when using functions in anat_fit_wf

Issue - State: open - Opened by yufang1039 2 months ago - 1 comment
Labels: bug

#3277 - Randomly fail when using functions in anat_fit_wf

Issue - State: open - Opened by yufang1039 2 months ago
Labels: bug

#3276 - Applying multiple pairs of PEPOLAR-style field maps with `B0Field*` fails

Issue - State: open - Opened by tsalo 2 months ago
Labels: bug, sdc

#3276 - Applying multiple pairs of PEPOLAR-style field maps with `B0Field*` fails

Issue - State: open - Opened by tsalo 2 months ago
Labels: bug, sdc

#3274 - Config file loading crashes when some array has mixed types

Issue - State: open - Opened by oesteban 3 months ago
Labels: bug

#3273 - Docker Run with SQLite3 Disk I/O Error

Issue - State: open - Opened by fenmeng123 3 months ago
Labels: bug

#3272 - Bump idna from 3.6 to 3.7

Pull Request - State: open - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#3271 - Enhancement: Add Euler number metric to structural QA report

Issue - State: open - Opened by jvarada over 6 years ago - 5 comments
Labels: help wanted

#3270 - RepetitionTime is not set in Nifti output on multi-echo data

Issue - State: closed - Opened by cmpetty 3 months ago - 2 comments
Labels: bug

#3269 - Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: open - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#3268 - poor functional brain mask

Issue - State: open - Opened by manzouri 3 months ago
Labels: bug

#3268 - poor functional brain mask

Issue - State: open - Opened by manzouri 3 months ago
Labels: bug

#3267 - Add templateflow to DatasetLinks

Pull Request - State: closed - Opened by tsalo 3 months ago - 3 comments

#3267 - Add templateflow to DatasetLinks

Pull Request - State: closed - Opened by tsalo 3 months ago - 3 comments

#3266 - fMRIprep not running

Issue - State: closed - Opened by aa84paris 3 months ago
Labels: bug

#3265 - Add `--session-id` parameter and support longitudinal output structure

Pull Request - State: open - Opened by tsalo 3 months ago - 1 comment

#3264 - ENH: Support named derivative paths

Pull Request - State: closed - Opened by tsalo 3 months ago - 1 comment

#3263 - Track proximal sources of functional GIFTIs

Pull Request - State: closed - Opened by tsalo 3 months ago - 2 comments

#3262 - Track Sources for standard-space outputs

Pull Request - State: closed - Opened by tsalo 3 months ago - 5 comments

#3261 - Track immediate `Sources` when possible

Issue - State: open - Opened by tsalo 3 months ago - 5 comments

#3260 - Allow `--derivatives` to be named

Issue - State: closed - Opened by tsalo 3 months ago - 1 comment
Labels: feature

#3259 - MNT: Verbatim copy of Apache license 2.0

Pull Request - State: closed - Opened by DimitriPapadopoulos 3 months ago

#3258 - ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version

Issue - State: open - Opened by WangYunHong98 4 months ago - 8 comments
Labels: bug

GitHub / nipreps/fmriprep issues and pull requests