nipreps/fmriprep issues and pull requests

#3231 - Add motion parameter units to confounds sidecar

Issue - State: closed - Opened by tsalo 5 months ago - 2 comments
Labels: feature

#3231 - Add motion parameter units to confounds sidecar

Issue - State: closed - Opened by tsalo 5 months ago - 2 comments
Labels: feature

#3230 - Problem during Node gen_avg - The xxx trait of a VolregOutputSpec instance must be a pathlike object or string

Issue - State: closed - Opened by LucieLenglart 5 months ago - 3 comments
Labels: bug, needs-mre

#3229 - Wrong fieldmap correction in 23.2.0 using opposite PE images

Issue - State: open - Opened by alexsayal 5 months ago - 9 comments
Labels: sdc

#3228 - Wrong output dimensions

Issue - State: open - Opened by adamnarai 5 months ago - 4 comments
Labels: bug

#3228 - Wrong output dimensions

Issue - State: open - Opened by adamnarai 5 months ago - 4 comments
Labels: bug

#3227 - Run Multiple Subjects in a Loop and fmriprep Picked the Wrong Subject's Jason File

Issue - State: closed - Opened by xxnagit 5 months ago - 2 comments
Labels: bug

#3227 - Run Multiple Subjects in a Loop and fmriprep Picked the Wrong Subject's Jason File

Issue - State: closed - Opened by xxnagit 5 months ago - 2 comments
Labels: bug

#3226 - MNT: Update environment pins

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

#3225 - Flag to align Freesurfer T1w and fMRIPrep T1w spaces

Issue - State: closed - Opened by butellyn 5 months ago - 2 comments

#3224 - fmriprep23.2 '--level minimal' fails with 'anat_to_template_Warped.nii.gz' not available

Issue - State: closed - Opened by FeHoff 5 months ago - 3 comments
Labels: bug

#3223 - FIX: delete summary from functional report when separated by sessions

Pull Request - State: closed - Opened by celprov 5 months ago

#3222 - Bump cryptography from 41.0.7 to 42.0.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 2 comments
Labels: dependencies, python

#3222 - Bump cryptography from 41.0.7 to 42.0.0

Pull Request - State: open - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, python

#3221 - STY: Lint and style check full repository

Pull Request - State: closed - Opened by effigies 5 months ago - 1 comment

#3220 - recon-all randomly fails for the exact same data (fmriprep-docker)

Issue - State: open - Opened by isacdaavid 5 months ago - 2 comments
Labels: bug

#3220 - recon-all randomly fails for the exact same data (fmriprep-docker)

Issue - State: closed - Opened by isacdaavid 5 months ago - 3 comments
Labels: bug

#3219 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, github_actions

#3218 - citation from 23.0.1 contains a duplicate paragraph with one difference

Issue - State: closed - Opened by burdinskid13 5 months ago - 2 comments
Labels: bug

#3217 - add citation generator for various citation styles

Issue - State: closed - Opened by burdinskid13 5 months ago - 1 comment

#3217 - add citation generator for various citation styles

Issue - State: closed - Opened by burdinskid13 5 months ago - 1 comment

#3216 - v23.2.0 wrong pixdim4 (TR)

Issue - State: closed - Opened by cni-md 5 months ago
Labels: bug

#3215 - FIX: Support lists in bids filter file containing `null` or `*`

Pull Request - State: closed - Opened by tsalo 5 months ago - 1 comment

#3214 - Support `null` and `*` in lists in `--bids-filter-file`

Issue - State: closed - Opened by tsalo 5 months ago - 2 comments

#3213 - Bump pillow from 10.1.0 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#3212 - Error running fmriprep on HCP data

Issue - State: open - Opened by DanielDiGiovanni-py 6 months ago - 5 comments
Labels: question

#3212 - Error running fmriprep on HCP data

Issue - State: open - Opened by DanielDiGiovanni-py 6 months ago - 5 comments
Labels: question

#3211 - Issues with reports after migrating to NiReports

Issue - State: open - Opened by oesteban 6 months ago - 2 comments
Labels: bug

#3211 - Issues with reports after migrating to NiReports

Issue - State: open - Opened by oesteban 6 months ago - 3 comments
Labels: bug

#3210 - TST: Update test to reflect new report generation behavior

Pull Request - State: open - Opened by mgxd 6 months ago - 4 comments

#3210 - TST: Update test to reflect new report generation behavior

Pull Request - State: closed - Opened by mgxd 6 months ago - 4 comments

#3209 - The test for crash file count on ds054 requires fixing.

Issue - State: closed - Opened by celprov 6 months ago

#3209 - The test for crash file count on ds054 requires fixing.

Issue - State: open - Opened by celprov 6 months ago

#3208 - ENH: Leverage T2w if available for BOLD -> anat coregistration

Pull Request - State: closed - Opened by mgxd 6 months ago - 1 comment

#3208 - ENH: Leverage T2w if available for BOLD -> anat coregistration

Pull Request - State: open - Opened by mgxd 6 months ago - 1 comment

#3207 - Separate count of crash files from count of error in report generation

Issue - State: open - Opened by celprov 6 months ago

#3207 - Separate count of crash files from count of error in report generation

Issue - State: closed - Opened by celprov 6 months ago - 1 comment

#3206 - STY: Adopt ruff for linting and formatting

Pull Request - State: closed - Opened by effigies 6 months ago - 3 comments

#3206 - STY: Adopt ruff for linting and formatting

Pull Request - State: open - Opened by effigies 6 months ago - 1 comment

#3205 - DOC: clarify `--dvars-spike-threshold` uses standardized DVARS

Pull Request - State: closed - Opened by htwangtw 6 months ago - 2 comments

#3205 - DOC: clarify `--dvars-spike-threshold` uses standardized DVARS

Pull Request - State: closed - Opened by htwangtw 6 months ago - 2 comments

#3204 - Clarify: `--dvars-spike-threshold` uses standardised dvars rather than dvars in online docs

Issue - State: closed - Opened by htwangtw 6 months ago - 1 comment
Labels: documentation

#3204 - Clarify: `--dvars-spike-threshold` uses standardised dvars rather than dvars in online docs

Issue - State: closed - Opened by htwangtw 6 months ago - 1 comment
Labels: documentation

#3203 - fMRI prep error on magnitude1 fieldmap in /extra_data folders despite .bidsignore file including /extra_data folder

Issue - State: open - Opened by lianneremie 6 months ago - 7 comments
Labels: bug

#3202 - Re-enable anat fasttrack for dataset without t1w

Pull Request - State: closed - Opened by bpinsard 6 months ago - 6 comments

#3201 - 23.2.0 breaks anat-fast-track on dataset without T1w

Issue - State: closed - Opened by bpinsard 6 months ago
Labels: bug

#3200 - fsaverage being deleted when running multiple subjects in parallel

Issue - State: closed - Opened by oricon 6 months ago - 4 comments
Labels: bug

#3199 - Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#3199 - Bump jinja2 from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#3198 - REL: 23.2.0

Pull Request - State: closed - Opened by effigies 6 months ago - 1 comment

#3197 - PIN: sdcflows @ rel/2.8.0

Pull Request - State: closed - Opened by effigies 6 months ago

#3196 - Add host information to dataset description

Issue - State: open - Opened by effigies 6 months ago

#3195 - aCompcor ROI Mask - GM Voxels

Issue - State: open - Opened by demidenm 6 months ago - 12 comments
Labels: bug

#3194 - MNT: Apply Repo-Review suggestions

Pull Request - State: closed - Opened by DimitriPapadopoulos 7 months ago - 1 comment

#3193 - freesurfer_home TraitError

Issue - State: open - Opened by omerday 7 months ago - 1 comment
Labels: bug

#3192 - slice timing correction failed

Issue - State: open - Opened by sarahfan128 7 months ago - 5 comments

#3191 - ENH: separate anatomical and functional reports per session for densely sampled dataset

Pull Request - State: closed - Opened by celprov 7 months ago - 7 comments

#3190 - CIFTI Pipeline .surf.gii larger than .dtseries.nii

Issue - State: open - Opened by amirhusseinab 7 months ago - 2 comments
Labels: bug

#3189 - fMRIPrep v23.2.0a1 cannot find my T1s "no attribute 'T1w_preproc'"

Issue - State: closed - Opened by cmpetty 7 months ago - 2 comments
Labels: bug

#3188 - Update development environment docs

Issue - State: open - Opened by effigies 7 months ago
Labels: documentation

#3186 - ENH: Allow --ignore fmap-jacobian to disable Jacobian determinant modulation during fieldmap correction

Pull Request - State: closed - Opened by effigies 7 months ago - 2 comments

#3185 - MNT: flake8/black/isort → ruff

Pull Request - State: closed - Opened by DimitriPapadopoulos 7 months ago

#3184 - MNT: Load reportlets interfaces from nireports rather than niworkflows

Pull Request - State: closed - Opened by effigies 7 months ago - 4 comments

#3183 - v. 23.2.0a2 SDC TOPUP odd results

Issue - State: closed - Opened by manuegrx 7 months ago - 3 comments
Labels: bug

#3183 - v. 23.2.0a2 SDC TOPUP odd results

Issue - State: open - Opened by manuegrx 7 months ago - 2 comments
Labels: bug

#3182 - Revert "MAINT: load reportlets interfaces from nireports rather than niworkflows"

Pull Request - State: closed - Opened by effigies 7 months ago - 1 comment

#3181 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, github_actions

#3180 - FIX: Restore --ignore sbref functionality

Pull Request - State: closed - Opened by effigies 7 months ago - 1 comment

#3179 - FIX: Retrieve atlas ROIs at requested density

Pull Request - State: closed - Opened by effigies 7 months ago - 3 comments

#3178 - Wrong atlas density for --cifti-output 170k

Issue - State: closed - Opened by xingyu-liu 7 months ago - 2 comments
Labels: bug

#3177 - RF: Load report assembler from nireports

Pull Request - State: closed - Opened by celprov 7 months ago - 11 comments

#3176 - MAINT: load reportlets interfaces from nireports rather than niworkflows

Pull Request - State: closed - Opened by celprov 7 months ago - 3 comments

#3175 - FIX: Keep minctracc [skip ci]

Pull Request - State: closed - Opened by effigies 7 months ago

#3174 - Bash is not running and gives no output

Issue - State: closed - Opened by connectomeclara 7 months ago - 3 comments

#3172 - RPT: Rename CSF/WM confounds in fMRIPlot

Pull Request - State: closed - Opened by tsalo 7 months ago - 1 comment

#3171 - Exclude non-steady-state volumes from confound correlation plot

Pull Request - State: closed - Opened by tsalo 7 months ago - 4 comments

#3170 - Separate goodvoxels mask creation from fsLR resampling

Pull Request - State: closed - Opened by tsalo 7 months ago - 2 comments
Labels: refactoring, CIFTI / Grayordinates

#3169 - Support predefined goodvoxels mask in `init_bold_fsLR_resampling_wf`

Issue - State: closed - Opened by tsalo 7 months ago - 2 comments
Labels: CIFTI / Grayordinates

#3168 - Goodvoxels mask no longer written out in 23.2.0a2

Issue - State: closed - Opened by tsalo 7 months ago - 5 comments
Labels: bug, CIFTI / Grayordinates

#3167 - Does the current version of fmriprep support the output of 32K GIfTI data?

Issue - State: closed - Opened by Luoyu-Wang 7 months ago - 4 comments
Labels: documentation

#3166 - Exclude echo entity from optimally combined derivatives

Pull Request - State: closed - Opened by tsalo 7 months ago - 4 comments

#3165 - Optimally combined ME-EPI CIFTI derivatives incorrectly have "echo" entity in filename

Issue - State: closed - Opened by madisoth 7 months ago - 3 comments
Labels: bug, me-epi, multiecho

#3164 - output preprocessed T2 in anat derivatives directory

Issue - State: closed - Opened by moser297 7 months ago - 4 comments

#3163 - Coregistration failing randomly between tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz and SBref

Issue - State: open - Opened by julfou81 7 months ago - 1 comment
Labels: bug

#3162 - fMRIPrep next preliminary results

Issue - State: closed - Opened by effigies 7 months ago - 1 comment
Labels: next

#3161 - Bump cryptography from 41.0.5 to 41.0.6

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 3 comments
Labels: dependencies, python

#3160 - 'DynamicTraitedSpec' object has no attribute 'T1w_preproc'

Issue - State: closed - Opened by juansanchezpena 7 months ago - 1 comment
Labels: bug

#3159 - FIX: Disable boldref-space outputs unless requested

Pull Request - State: closed - Opened by effigies 7 months ago - 1 comment
Labels: next

#3158 - fieldmap-less SDC in v. 23.2.0a2 producing odd/distorted results

Issue - State: closed - Opened by atkinsonap 8 months ago - 3 comments
Labels: bug