khanlab/hippunfold issues and pull requests

#273 - How to know when subjects are fully processed?

Issue - State: closed - Opened by vnbcs about 1 year ago - 1 comment

#272 - another error on the ds002168 example dataset

Issue - State: closed - Opened by CogBrainHealthLab about 1 year ago - 2 comments

#271 - logo

Pull Request - State: closed - Opened by jordandekraker about 1 year ago
Labels: documentation

#270 - Add testing for other python versions

Pull Request - State: closed - Opened by kaitj about 1 year ago - 2 comments
Labels: maintenance

#269 - new branch for cleaner PR

Pull Request - State: closed - Opened by jordandekraker over 1 year ago - 2 comments

#268 - resources to osf repo

Pull Request - State: closed - Opened by jordandekraker over 1 year ago - 1 comment

#267 - Sampling functional data for the dentate gyrus

Issue - State: closed - Opened by vipfa100 over 1 year ago - 2 comments

#266 - Error running ds002168 (example) subject: Potentially with symbolic links?

Issue - State: closed - Opened by jlhanson5 over 1 year ago - 15 comments

#265 - Update .readthedocs.yml

Pull Request - State: closed - Opened by akhanf over 1 year ago

#264 - Marmunfold

Pull Request - State: closed - Opened by akhanf over 1 year ago - 19 comments
Labels: wontfix

#263 - adds missing T2w dHCP template to configfile

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: bug

#262 - Change in dependencies

Pull Request - State: closed - Opened by akhanf over 1 year ago - 3 comments
Labels: maintenance

#261 - Fix session bug

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: bug

#260 - Latest tag

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: documentation

#259 - Question: QC/unetf3d_dice.tsv

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

#258 - Tutorial for transforming BigBrain to MNI

Issue - State: closed - Opened by andreifoldes over 1 year ago - 3 comments

#257 - sample functional data along surface

Issue - State: closed - Opened by vipfa100 over 1 year ago - 9 comments

#256 - rename histologyReference2023 to multihist7

Pull Request - State: closed - Opened by akhanf over 1 year ago - 2 comments
Labels: enhancement

#255 - fixes bug introduced in unfold_reg by reverting

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: bug

#254 - Naming of histologyReference2023

Issue - State: closed - Opened by akhanf over 1 year ago - 3 comments

#253 - label.gii and dlabel.nii files for subfields are corrupt in v1.3.0+

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

#252 - Update README.md

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: documentation

#251 - replace use of HTTP.remote() with wget

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: bug

#250 - Update README.md

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: documentation

#249 - added neonate_v2 model, minor workflow update for it

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: maintenance

#248 - process HCP fmri on hippunfold results

Issue - State: closed - Opened by raywell627 over 1 year ago - 2 comments

#247 - Download models inside workflow

Pull Request - State: closed - Opened by akhanf over 1 year ago - 3 comments
Labels: documentation, maintenance

#246 - Update README.md

Pull Request - State: closed - Opened by akhanf over 1 year ago
Labels: documentation

#245 - zero value vertices on dentate gyrus

Issue - State: closed - Opened by HusBunia over 1 year ago - 4 comments

#244 - Synthseg model

Pull Request - State: closed - Opened by jordandekraker over 1 year ago - 1 comment
Labels: enhancement

#243 - Synthseg model

Pull Request - State: closed - Opened by jordandekraker over 1 year ago - 1 comment

#242 - curvature was producing a few outlier extreme values

Pull Request - State: closed - Opened by jordandekraker over 1 year ago
Labels: bug

#241 - DG surface contains self-intersection

Issue - State: closed - Opened by debinz over 1 year ago - 6 comments

#240 - Warps fix

Pull Request - State: closed - Opened by jordandekraker over 1 year ago - 2 comments
Labels: bug

#239 - small bug present when visualizing with freeview

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

#238 - quality check git action fix

Pull Request - State: closed - Opened by jordandekraker almost 2 years ago

#237 - Fix quality action

Pull Request - State: closed - Opened by kaitj almost 2 years ago
Labels: bug

#236 - ensure use of Laplace coords follows gm mask

Pull Request - State: closed - Opened by jordandekraker almost 2 years ago

#235 - Maskcontrain

Pull Request - State: closed - Opened by jordandekraker almost 2 years ago

#234 - updates from master branch

Pull Request - State: closed - Opened by jordandekraker almost 2 years ago

#233 - Converting inner/outer surface files to WM and pial format in Freesurfer

Issue - State: closed - Opened by khazarAhmadi almost 2 years ago - 3 comments

#232 - T1T2w model file/url was missing from the config

Pull Request - State: closed - Opened by akhanf almost 2 years ago
Labels: bug

#231 - Bug in crop native space

Issue - State: closed - Opened by akhanf almost 2 years ago - 1 comment

#230 - fix bug in crop native box

Pull Request - State: closed - Opened by akhanf almost 2 years ago - 1 comment
Labels: bug

#229 - Cyclic dependency on rule warp_gii_to_native.

Issue - State: closed - Opened by debinz almost 2 years ago - 11 comments

#228 - Unfold reg

Pull Request - State: closed - Opened by jordandekraker almost 2 years ago - 5 comments
Labels: major

#227 - Add accepted in eLife mention and link to readme

Pull Request - State: closed - Opened by akhanf about 2 years ago
Labels: documentation

#226 - fix for input type in dseg qc

Pull Request - State: closed - Opened by jordandekraker about 2 years ago
Labels: bug

#225 - bugfix for cropref

Pull Request - State: closed - Opened by jordandekraker about 2 years ago
Labels: bug

#224 - defined in mm instead of vox

Pull Request - State: closed - Opened by jordandekraker about 2 years ago - 7 comments
Labels: enhancement

#223 - Note on autotop_deps

Pull Request - State: closed - Opened by jordandekraker over 2 years ago
Labels: documentation

#222 - Updates for Windows

Pull Request - State: closed - Opened by jordandekraker over 2 years ago
Labels: documentation

#221 - Download rule in the workflow

Pull Request - State: closed - Opened by akhanf over 2 years ago - 3 comments
Labels: enhancement

#220 - aligns laplace_coords.py behaviour to laplace_coords_withinit.py

Pull Request - State: closed - Opened by jordandekraker over 2 years ago - 3 comments
Labels: bug

#219 - update docs for running singularity in linux

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: documentation

#218 - Windows docker instructions

Issue - State: closed - Opened by jordandekraker over 2 years ago - 1 comment

#217 - missing subfield.dlabel.gii outputs

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

#216 - Added missing container for hippdwi_to_template

Pull Request - State: closed - Opened by kaitj over 2 years ago - 2 comments
Labels: bug

#215 - resample_hippdwi_to_template container missing

Issue - State: closed - Opened by kaitj over 2 years ago - 1 comment
Labels: bug

#214 - Update_documentation

Pull Request - State: closed - Opened by mcespedes99 over 2 years ago
Labels: documentation

#213 - updated deploy workflow with bumpversion changes

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: maintenance

#212 - Add DAG generation to a github action

Issue - State: open - Opened by akhanf over 2 years ago - 1 comment
Labels: maintenance, v2.0

#211 - bugfix: subfields label.gii wasn't being generated properly

Pull Request - State: closed - Opened by akhanf over 2 years ago - 1 comment
Labels: bug

#210 - added --version to CLI (via snakebids.yml)

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: enhancement

#209 - Test data

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: documentation

#208 - bugfix: subfield+tissue for new atlases, and tsv files

Pull Request - State: closed - Opened by akhanf over 2 years ago - 1 comment
Labels: bug

#207 - Extras moved to toolbox

Pull Request - State: closed - Opened by jordandekraker over 2 years ago - 1 comment
Labels: maintenance

#206 - Summary statistics of the surface metrics

Issue - State: open - Opened by romeopenheiro over 2 years ago - 4 comments
Labels: enhancement, good first issue

#205 - Multiple atlases updating docs & coding style

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: documentation

#204 - hippdwi bounding box for L and R flipped

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: bug

#203 - Unfolddentatetemplate patch

Pull Request - State: closed - Opened by jordandekraker over 2 years ago - 4 comments
Labels: maintenance

#202 - unfolded DG template not rectangular

Issue - State: closed - Opened by jordandekraker over 2 years ago

#201 - added missing canonical surfaces for label-dentate

Pull Request - State: closed - Opened by jordandekraker over 2 years ago - 3 comments
Labels: maintenance

#200 - allows output of subfields using multiple unfolded atlases

Pull Request - State: closed - Opened by jordandekraker over 2 years ago - 1 comment
Labels: enhancement

#199 - Update Dockerfile

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: maintenance

#198 - adds unsupported note for M1

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: documentation

#197 - run inference duration

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

#196 - long staging

Issue - State: closed - Opened by jordandekraker over 2 years ago - 2 comments
Labels: documentation

#195 - freeview formatted subfield label file

Pull Request - State: closed - Opened by jordandekraker over 2 years ago
Labels: enhancement

#194 - Drop generic copy_to_results rule

Pull Request - State: closed - Opened by akhanf over 2 years ago - 1 comment
Labels: maintenance

#193 - Cryptic error given when running hippunfold before `hippunfold_download_models` is run

Issue - State: closed - Opened by akhanf over 2 years ago - 3 comments
Labels: bug

#192 - Force creation of .snakebids file

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: bug

#191 - `.snakebids` file not found

Issue - State: closed - Opened by romeopenheiro over 2 years ago - 10 comments
Labels: bug

#190 - update snakebids dependency

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: maintenance

#189 - fixes group-level analysis

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: bug

#188 - group-level analysis broken

Issue - State: closed - Opened by akhanf over 2 years ago
Labels: bug

#187 - change --nnunet-disable-tta to --nnunet-enable-tta

Pull Request - State: closed - Opened by akhanf over 2 years ago
Labels: bug

#186 - Freesurfer atlas

Pull Request - State: closed - Opened by akhanf over 2 years ago - 4 comments
Labels: enhancement

#185 - test-time augmentation actually disabled by default

Issue - State: closed - Opened by akhanf over 2 years ago

#184 - expose crop_native_box as a config and CLI variable

Pull Request - State: closed - Opened by akhanf over 2 years ago - 3 comments
Labels: enhancement

#183 - doc updates

Pull Request - State: closed - Opened by akhanf over 2 years ago - 2 comments
Labels: documentation

#182 - Total Intracranial volume estimates

Issue - State: open - Opened by akhanf almost 3 years ago - 2 comments
Labels: enhancement

#181 - update release drafter

Pull Request - State: closed - Opened by akhanf almost 3 years ago
Labels: maintenance

#180 - bugfix for warps hemi-L

Pull Request - State: closed - Opened by jordandekraker almost 3 years ago - 8 comments
Labels: bug

#179 - added myelin map to docs

Pull Request - State: closed - Opened by akhanf almost 3 years ago
Labels: documentation

#178 - added rule to summarize surf metrics over subfields

Pull Request - State: closed - Opened by akhanf almost 3 years ago
Labels: enhancement

#177 - adds missing output space default

Pull Request - State: closed - Opened by akhanf almost 3 years ago
Labels: maintenance

#176 - Custom atlas

Pull Request - State: closed - Opened by akhanf almost 3 years ago - 10 comments
Labels: enhancement, breaking

#175 - CI updates, remove circleci, use github actions to build/push to dockerhub

Pull Request - State: closed - Opened by akhanf almost 3 years ago
Labels: maintenance

#174 - simplified outputs by concatenating label-hipp/dentate

Issue - State: closed - Opened by jordandekraker almost 3 years ago - 3 comments
Labels: enhancement

GitHub / khanlab/hippunfold issues and pull requests