yeatmanlab/pyAFQ issues and pull requests

#963 - DOC: How to run pyAFQ through qsiprep

Issue - State: open - Opened by arokem over 1 year ago - 1 comment

#962 - [ENH] add gpu tracking to pyAFQ

Pull Request - State: closed - Opened by 36000 over 1 year ago - 3 comments

#961 - [WIP, ENH, FIX] Re-organize the mapping code and remove ITK support

Pull Request - State: closed - Opened by 36000 over 1 year ago - 1 comment

#960 - no bundles?

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

#959 - Using preexisting ITK maps

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

#958 - HTTP Error 403: Forbidden

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

#957 - Export just the maps

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

#956 - BundleDict assignment doesn't work?

Issue - State: closed - Opened by arokem over 1 year ago - 5 comments

#955 - [FIX] Add max length constraint, b0 fix

Pull Request - State: closed - Opened by 36000 over 1 year ago

#954 - Understanding preprocessing steps needed for raw DTI data to be run through pyAFQ

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

#953 - [ENH/FIX] Improvements for finding the Visual Pathway

Pull Request - State: closed - Opened by 36000 over 1 year ago - 10 comments

#952 - Corpus Callosum is assumed to be in the center of the image in CSD modeling

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

#951 - BF: Calculate mean b0 instead of mean not-b0

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

#950 - [BUG] Should this have a tilde?

Issue - State: closed - Opened by 36000 over 1 year ago - 1 comment

#949 - Small documentation fixes, to improve auto-rendering of API docs.

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

#948 - Starting doc overhaul

Pull Request - State: closed - Opened by qiqiliang over 1 year ago - 4 comments

#947 - MAINT: pep517 => build.

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

#946 - [ENH] auto generate babyAFQ pipeline for qsiprep

Pull Request - State: closed - Opened by 36000 over 1 year ago

#945 - MAINT: Upgrade pytest as a start to tackling CI errors.

Pull Request - State: closed - Opened by arokem over 1 year ago - 3 comments

#944 - [FIX] Missing underscore in custom tissue property filenames

Pull Request - State: closed - Opened by 36000 almost 2 years ago

#943 - WIP: s3bids deprecation

Pull Request - State: open - Opened by arokem almost 2 years ago - 4 comments

#942 - Seed and Stop masked are saved before thresholding.

Issue - State: open - Opened by 36000 almost 2 years ago

#939 - Setting stop_mask to "ACT" raises an error at wrapper_as_img() in decorator.py

Issue - State: open - Opened by JiyeongHa almost 2 years ago

#938 - Raise more informative error for inconsistent inputs to AFQ.tractography.track ACT

Issue - State: open - Opened by arokem almost 2 years ago

#937 - [FIX] finally finish this SLR PR

Pull Request - State: closed - Opened by 36000 almost 2 years ago

#936 - [FIX] Import tract docs

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 5 comments

#935 - [Error]ParticipantAFQ

Issue - State: closed - Opened by sleeeeeeepy almost 2 years ago - 5 comments

#933 - using fsl data

Issue - State: closed - Opened by tstefancin almost 2 years ago

#932 - TST: Fixes another failing nightly test by setting the seed.

Pull Request - State: closed - Opened by arokem almost 2 years ago - 1 comment

#931 - Add fwDTI

Pull Request - State: closed - Opened by arokem almost 2 years ago - 7 comments

#930 - DOC: Fix the random seed for the OR example.

Pull Request - State: closed - Opened by arokem almost 2 years ago - 1 comment

#929 - TST: Fix a random seed for this test.

Pull Request - State: closed - Opened by arokem almost 2 years ago - 1 comment

#927 - fiber tracts clustered around midbrain

Issue - State: closed - Opened by iliana-karipidis almost 2 years ago

#926 - Test datasets are not valid BIDS datasets

Issue - State: open - Opened by arokem almost 2 years ago - 1 comment

#925 - Document integration with qsiprep

Issue - State: open - Opened by arokem almost 2 years ago

#924 - a error when downloading template

Issue - State: closed - Opened by RosieZho almost 2 years ago - 8 comments

#923 - [ENH] Allow pediatric bundledict and template to be accessed from config file.

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 1 comment

#922 - [FIX] Some pediatric bundle dict fixes

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 1 comment

#921 - Increase inclusion tolerance for pAF; add suffix for cmd_outputs

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 1 comment

#920 - set up file logger with timestamp

Pull Request - State: open - Opened by pierre-nedelec almost 2 years ago - 4 comments

#919 - [FIX] don't resample subject-space ROIs unless user provides something

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 8 comments

#918 - Segmenting only from endpoint ROIs

Issue - State: closed - Opened by arokem almost 2 years ago - 7 comments

#917 - `parallel_params` not passed into segmentation

Issue - State: closed - Opened by arokem almost 2 years ago - 5 comments

#916 - Document the direction of each bundle profile

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

#915 - `tract_profile` creation overwrites existing instead of appending

Issue - State: open - Opened by pierre-nedelec almost 2 years ago - 1 comment

#914 - Some logging improvements

Issue - State: open - Opened by 36000 almost 2 years ago - 5 comments

#913 - [FIX] put afq_metadata.toml in the correct spot

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 1 comment

#912 - [ENH] VOF endpoints don't include pAF endpoints

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 1 comment

#911 - [FIX] Updating DIPY tracking params

Pull Request - State: closed - Opened by 36000 almost 2 years ago - 10 comments
Labels: investigating

#910 - DOC: Adds an example of visualizations using FURY.

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

#909 - DOC: Document S3BIDS access examples.

Pull Request - State: closed - Opened by arokem about 2 years ago - 1 comment

#908 - Should we make s3bids its own library?

Issue - State: closed - Opened by arokem about 2 years ago - 2 comments

#907 - Replace all instances of PipelineDescription by GeneratedBy

Pull Request - State: closed - Opened by arokem about 2 years ago - 1 comment

#906 - Specific to bundle parameters for cleaning / lengths

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#905 - [FIX] correctly calculate min / max sl length, update step_size docs

Pull Request - State: closed - Opened by 36000 about 2 years ago - 7 comments

#904 - Add a version string to derivative folder name

Issue - State: open - Opened by arokem about 2 years ago

#903 - option for startpoint/endpoint density

Issue - State: open - Opened by jyeatman about 2 years ago
Labels: enhancement, good first issue, effort: low

#902 - [WIP] Add surface.py for tract <-> surface functionality

Pull Request - State: open - Opened by sambjohnson about 2 years ago - 2 comments

#901 - single start roi / single end roi / single waypoint functionality

Issue - State: closed - Opened by 36000 about 2 years ago

#900 - [ENH] Density task

Pull Request - State: closed - Opened by 36000 about 2 years ago - 7 comments

#899 - [WIP] towards bootstrap

Pull Request - State: closed - Opened by 36000 about 2 years ago

#898 - Added streamline filtering by primary orientation; other bundle definition fixes

Pull Request - State: closed - Opened by 36000 about 2 years ago - 1 comment

#897 - preproc_pipeline should not be optional

Issue - State: open - Opened by 36000 about 2 years ago

#896 - Add `dki_tortuosity`

Issue - State: open - Opened by arokem about 2 years ago

#895 - loky potential memory leak during segmentation

Issue - State: closed - Opened by 36000 about 2 years ago

#894 - Consider auto-generating dataset_description files

Issue - State: open - Opened by jyeatman about 2 years ago

#893 - New pybids default: {"validate": False}

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#892 - Memory error in segmentation

Issue - State: closed - Opened by 36000 about 2 years ago

#891 - clobber

Issue - State: closed - Opened by jyeatman about 2 years ago - 2 comments

#890 - Prioritize fiber groups

Issue - State: open - Opened by jyeatman about 2 years ago

#889 - undocumented argument stat=stat

Issue - State: closed - Opened by jyeatman about 2 years ago - 2 comments

#888 - move computation within while loop for cleaning

Issue - State: closed - Opened by jyeatman about 2 years ago - 2 comments

#887 - Bug in cleaning fibers

Issue - State: closed - Opened by jyeatman about 2 years ago
Labels: bug

#886 - clean by endpoints should not be generator (personal opinion)

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#885 - personal opinion: simplify segmentation class

Issue - State: closed - Opened by 36000 about 2 years ago - 3 comments

#884 - personal opinion: we should not output the pre-cleaned derivatives (what's the point?)

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#883 - roiImage should be able to "OR" endpoints and includes (maybe bring back the combine?)

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#882 - dont say filtered by prob map if using default

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#881 - [FIX] cmd output only run on our files

Pull Request - State: closed - Opened by 36000 about 2 years ago - 3 comments

#880 - Added streamline filtering by primary orientation

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

#879 - visualization library should accept stateful tractogram, not just segmentedSFT

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#878 - also export endpoint ROI with start/end

Issue - State: closed - Opened by 36000 about 2 years ago - 1 comment

#877 - export_all option to not make combined profile ; expose export_all params to CLI

Issue - State: open - Opened by 36000 about 2 years ago

#876 - organize stanford hardi function should return path

Issue - State: open - Opened by 36000 about 2 years ago

#875 - [DOC] add pyafq overview desciption

Pull Request - State: closed - Opened by 36000 about 2 years ago - 1 comment

#874 - FIX: nightly broken online, but passes locally

Pull Request - State: closed - Opened by 36000 about 2 years ago - 3 comments

#873 - Fix nightly tests

Pull Request - State: closed - Opened by 36000 about 2 years ago - 4 comments

#872 - Error handling broken

Issue - State: closed - Opened by arokem about 2 years ago

#870 - Update to generate by for BIDS

Pull Request - State: closed - Opened by 36000 about 2 years ago - 4 comments

#867 - Set logger levels to INFO

Pull Request - State: closed - Opened by arokem about 2 years ago - 6 comments

#866 - Not finding DWI when BIDS structure doesn't include sessions?

Issue - State: closed - Opened by arokem about 2 years ago - 2 comments

#864 - Save profiles of the "lower triangular" for DKI

Issue - State: closed - Opened by arokem about 2 years ago

#861 - [DOC] add interactive bundle viz to OR example

Pull Request - State: closed - Opened by 36000 about 2 years ago - 5 comments

#859 - Reorder segmentation criteria

Issue - State: closed - Opened by arokem about 2 years ago - 1 comment

#856 - SLR nightly test seems to fail intermittently

Issue - State: closed - Opened by arokem about 2 years ago

#843 - Custom Scalars Error

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

GitHub / yeatmanlab/pyAFQ issues and pull requests