nipreps/dmriprep issues and pull requests

#204 - gen_eddy_files failed to run

Issue - State: open - Opened by LangFiL 7 months ago
Labels: bug

#203 - FIX: typo in omp_threads

Pull Request - State: closed - Opened by celprov about 1 year ago

#202 - [WARNING] Citeproc: citation eddy not found

Issue - State: open - Opened by celprov about 1 year ago
Labels: bug

#201 - FIX: fix typo that prevented to ignore fieldmaps

Pull Request - State: closed - Opened by celprov about 1 year ago - 1 comment

#200 - No dwi derivatives in output directory

Issue - State: closed - Opened by maryjis over 1 year ago - 1 comment
Labels: bug

#198 - The tutorial of dMRIprep singularity using was not work

Issue - State: closed - Opened by alienx-zero over 1 year ago - 1 comment

#197 - dMRIPrep generalizations (m 12-24)

Issue - State: open - Opened by esavary over 1 year ago

#196 - dMRIPrep roadmap (m3-9)

Issue - State: open - Opened by esavary over 1 year ago

#195 - MAINT: Rotate CircleCI secrets and setup up org-level context

Pull Request - State: open - Opened by oesteban almost 2 years ago

#194 - Running problem of a file "scans.json"

Issue - State: open - Opened by Clancy-wu over 2 years ago

#193 - Mif conversion

Pull Request - State: closed - Opened by GalKepler over 2 years ago

#192 - Keeping track of fMRIPrep.

Pull Request - State: open - Opened by GalKepler over 2 years ago - 1 comment

#191 - [ENH] Keep up with fMRIPrep's infrastructure

Issue - State: open - Opened by GalKepler over 2 years ago

#190 - [ENH] Mrtrix3-based pipeline

Issue - State: open - Opened by GalKepler over 2 years ago

#189 - Qa

Pull Request - State: closed - Opened by GalKepler over 2 years ago - 1 comment

#188 - Most of the mrtrix-based pipeline is done

Pull Request - State: closed - Opened by GalKepler over 2 years ago

#187 - added bids filterring functionality to data collection process

Pull Request - State: closed - Opened by GalKepler over 2 years ago - 2 comments

#185 - MAINT: Revise dependencies

Pull Request - State: open - Opened by oesteban almost 3 years ago

#184 - MAINT: Use the base ``nipreps/miniconda`` image

Pull Request - State: open - Opened by oesteban almost 3 years ago - 2 comments

#183 - First LTS release

Issue - State: open - Opened by oesteban about 3 years ago
Labels: NiPreps Grant

#182 - Build comprehensive integration and stress testing into dMRIPrep

Issue - State: open - Opened by oesteban about 3 years ago
Labels: NiPreps Grant

#181 - Integration of eddymotion

Issue - State: open - Opened by oesteban about 3 years ago
Labels: NiPreps Grant

#180 - Benchmark the accuracy of image co-registration to the same subject's T1w image

Issue - State: open - Opened by oesteban about 3 years ago
Labels: NiPreps Grant

#179 - Gibbs ringing - estimation and correction workflow

Issue - State: open - Opened by oesteban about 3 years ago
Labels: NiPreps Grant

#178 - DOC: Roadmap update

Pull Request - State: open - Opened by oesteban about 3 years ago - 1 comment

#177 - MAINT: Update several CircleCI settings

Pull Request - State: closed - Opened by oesteban about 3 years ago

#176 - MAINT: Pin h5py separately.

Pull Request - State: closed - Opened by arokem about 3 years ago - 2 comments

#175 - FIX: Output eddy parameter files to work dir instead of input dir

Pull Request - State: closed - Opened by josephmje about 3 years ago

#174 - MAINT: Adopt new NiPreps' governance model

Pull Request - State: open - Opened by oesteban about 3 years ago - 4 comments

#172 - Error on "gen_eddy_files"

Issue - State: open - Opened by h-w-k over 3 years ago - 1 comment

#171 - Investigate SD estimation with the two polarities of DWI on ds001771

Issue - State: open - Opened by oesteban over 3 years ago

#170 - Reference workflow - extreme clipping in ds000206

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

#169 - ENH: Use NiWorkflows' EPI-reference workflow

Pull Request - State: closed - Opened by oesteban over 3 years ago - 7 comments

#168 - SDC - Horrible co-registration of b=0 reference and EPI reference

Issue - State: open - Opened by oesteban over 3 years ago - 1 comment
Labels: bug

#167 - DOC: Add copyright note to every file, add NOTICE file, update Dockefile

Pull Request - State: closed - Opened by oesteban over 3 years ago

#166 - ENH: Write out b=0 reference(s)

Pull Request - State: closed - Opened by josephmje over 3 years ago

#165 - No folder output directory of dwi created

Issue - State: closed - Opened by nabaruns over 3 years ago - 4 comments

#164 - FIX: Clear cache for ds000206 dataset

Pull Request - State: closed - Opened by josephmje over 3 years ago

#163 - DOC: Update external dependency versions

Pull Request - State: closed - Opened by josephmje over 3 years ago - 2 comments

#162 - Reportlet to check on eddy/emc results

Issue - State: open - Opened by oesteban over 3 years ago

#161 - Write out b=0 reference(s)

Issue - State: closed - Opened by oesteban over 3 years ago

#160 - using dMRIprep for the first time

Issue - State: closed - Opened by Meryam1985 over 3 years ago - 3 comments

#159 - eddy: msg=ECScanManager::GetShellIndicies: Data not shelled

Issue - State: closed - Opened by levchenkoegor over 3 years ago - 3 comments

#158 - FIX: PEPOLAR & mapped fieldmaps not showing up in reports

Pull Request - State: closed - Opened by oesteban over 3 years ago

#157 - Estimated fieldmap present in reports only for fieldmap-less

Issue - State: closed - Opened by oesteban over 3 years ago
Labels: bug, impact: high, effort: low, depends: SDCFlows

#156 - FIX: Update to new NiWorkflows API

Pull Request - State: closed - Opened by oesteban over 3 years ago

#155 - MAINT: Refactor Dockerfile with better use of miniconda

Pull Request - State: closed - Opened by oesteban over 3 years ago - 1 comment

#154 - ENH: Move pandoc execution to the end of the runtime

Pull Request - State: closed - Opened by oesteban over 3 years ago - 2 comments

#153 - ENH: fieldmap-less integration from SDCFlows 2.0

Pull Request - State: closed - Opened by oesteban over 3 years ago - 1 comment

#152 - MAINT: Update SDCFlows pinning to the latest 2.0.0 release

Pull Request - State: closed - Opened by oesteban over 3 years ago

#151 - FIX: Change in _svgutils_ API (0.3.2) breaks our reportlet generation

Pull Request - State: closed - Opened by oesteban over 3 years ago

#150 - ENH: Add number of volumes per b-value to QC report

Pull Request - State: open - Opened by josephmje over 3 years ago - 8 comments

#148 - DOC: Add FSL ``topup`` reference in citation boilerplate

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#147 - DOC: Revise dMRIPrep's road-map

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 1 comment

#146 - FIX/MAINT: Drop Python 3.6 + Revise Python environment (versions pinned) in Dockerfile

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 1 comment

#145 - Broken numpy dependency for scikit-image installation

Issue - State: closed - Opened by oesteban almost 4 years ago

#144 - ENH: Temporary integration of FSL eddy

Pull Request - State: closed - Opened by slimnsour almost 4 years ago - 18 comments

#143 - DOC: change "functional" to "diffusion"

Pull Request - State: closed - Opened by josephmje almost 4 years ago - 1 comment

#142 - FIX: Honor ``--nprocs`` flag

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#141 - FIX: Correctly check SDCFlows registry of ``IntendedFor`` files

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 3 comments

#140 - ENH: Connect fieldmap estimation to preprocessing pipeline of individual DWI runs

Pull Request - State: closed - Opened by josephmje almost 4 years ago - 7 comments

#139 - Temporary integration of FSL eddy

Issue - State: closed - Opened by oesteban almost 4 years ago - 1 comment
Labels: enhancement, impact: high, effort: medium

#138 - ENH: Refactor workflow for simplicity - explicit iteration over DWIs

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#137 - ENH: Run fieldmap estimation using SDCFlows 2.0

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 1 comment

#135 - MAINT: Move packaging tests from TravisCI to GitHub Actions

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#134 - MAINT: Move test data to a full-datalad settings

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#133 - updated edickie's affiliation

Pull Request - State: closed - Opened by edickie almost 4 years ago

#132 - Roundup of denoising and unringing algorithms from ISMRM

Issue - State: open - Opened by josephmje almost 4 years ago - 3 comments
Labels: enhancement

#131 - ENH: Use ``bbregister`` upstreamed to NiWorkflows, with sloppy mode

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#130 - STY/MAINT: Preparing the first large overhaul of dMRIPrep

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 1 comment

#129 - ENH: Add number of volumes per b-value to QC report

Pull Request - State: closed - Opened by josephmje almost 4 years ago - 3 comments

#128 - Using `DiffusionGradientTable` on HCP-style acquisition

Issue - State: open - Opened by josephmje almost 4 years ago - 3 comments

#127 - DOC: Update readme and delete contributing guidelines in favour of nipreps website

Pull Request - State: closed - Opened by josephmje almost 4 years ago - 2 comments

#126 - MAINT: Adding J. Veraart to the contributors list

Pull Request - State: closed - Opened by oesteban almost 4 years ago

#125 - ENH: Port bbregister T1-to-dwi registration from fmriprep

Pull Request - State: closed - Opened by slimnsour almost 4 years ago - 6 comments

#124 - DOC: Add base SVG file for the "figure1" (aka the workflow) flowchart

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 3 comments
Labels: documentation

#123 - REL: 0.3.0

Pull Request - State: closed - Opened by oesteban almost 4 years ago - 1 comment

#122 - BrainHack Donostia 2020 / Tutorial

Issue - State: closed - Opened by oesteban almost 4 years ago - 1 comment

#121 - Benchmarking preprocessing choices with validation data

Issue - State: open - Opened by dPys about 4 years ago
Labels: impact: high, effort: high, validation / evaluation

#120 - Adds link to NH video.

Pull Request - State: closed - Opened by arokem about 4 years ago - 3 comments

#119 - Tutorial Proposal for ISBI (deadline: 09/25)

Issue - State: closed - Opened by oesteban about 4 years ago - 12 comments

#118 - Meeting 09/29 - Agenda

Issue - State: closed - Opened by oesteban about 4 years ago - 1 comment

#117 - Rotating oblique volumes and bvecs

Issue - State: open - Opened by josephmje about 4 years ago - 1 comment

#116 - Revise Roadmap

Issue - State: closed - Opened by oesteban about 4 years ago

#115 - Port T1w-to-dwi registration from fMRIPrep (only bbregister)

Issue - State: closed - Opened by oesteban about 4 years ago
Labels: good first issue, impact: medium, effort: medium

#114 - UserWarning: Casting data from int16 to float32

Issue - State: open - Opened by levchenkoegor about 4 years ago
Labels: bug

#113 - `n4_correct` from `early_b0ref_wf` fails on some subjects

Issue - State: open - Opened by josephmje about 4 years ago - 4 comments
Labels: bug

#112 - Link to Oscar's NeuroHackademy tutorial in the documentation

Issue - State: closed - Opened by arokem about 4 years ago

#111 - fieldmap-free distortion correction

Issue - State: closed - Opened by h-w-k over 4 years ago - 4 comments
Labels: impact: high, effort: high, depends: SDCFlows

#106 - MAINT: Remove the leftovers of AFQ in ``.afq/``

Pull Request - State: closed - Opened by oesteban over 4 years ago - 3 comments

#104 - Registration tools (arokem)

Pull Request - State: open - Opened by arokem over 4 years ago - 4 comments

#101 - FIX: Minor refactor of DWI/brainmasks utilities and dtypes

Pull Request - State: closed - Opened by oesteban over 4 years ago - 3 comments

#96 - Framewise displacement calculation

Issue - State: open - Opened by oesteban over 4 years ago - 1 comment
Labels: impact: high, effort: medium

#94 - Head-motion estimation for HMC

Issue - State: closed - Opened by oesteban over 4 years ago - 3 comments
Labels: impact: high, effort: high

#78 - [ENH] Registration tools

Pull Request - State: open - Opened by dPys over 4 years ago - 8 comments

#77 - [ENH] Add emc-related helper functions - images

Pull Request - State: open - Opened by dPys over 4 years ago - 10 comments

#76 - [ENH] Add emc helper functions - vectors

Pull Request - State: open - Opened by dPys over 4 years ago - 3 comments

#73 - [ENH] - extra bval parsing for number of shells

Pull Request - State: open - Opened by edickie over 4 years ago - 6 comments

#70 - [ENH] A doctested grouping algorithm

Pull Request - State: closed - Opened by mattcieslak over 4 years ago - 6 comments

#64 - Determine number of shells

Issue - State: closed - Opened by oesteban over 4 years ago - 2 comments

GitHub / nipreps/dmriprep issues and pull requests