scilus/scilpy issues and pull requests

#714 - ENH: Verbose tracking

Pull Request - State: closed - Opened by EmmaRenauld almost 2 years ago - 10 comments

#713 - Adding import matplotlib to assign_custom_color_to_tractogram

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

#712 - Upgrade dipy to 1.7.0

Pull Request - State: closed - Opened by CHrlS98 almost 2 years ago - 1 comment

#711 - pyproject toml

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

#710 - Fix validate BIDS

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

#709 - Fix: Add bundle to scores if it was not found

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

#708 - Refactor asym_odf_metrics script

Pull Request - State: closed - Opened by CHrlS98 almost 2 years ago - 3 comments

#707 - RBx with FSS

Pull Request - State: closed - Opened by frheault almost 2 years ago - 9 comments

#706 - Unit test tractogram operations

Pull Request - State: closed - Opened by EmmaRenauld almost 2 years ago - 3 comments

#705 - Display masks as contours in screenshots

Pull Request - State: closed - Opened by AlexVCaron almost 2 years ago - 12 comments

#704 - Adding legacy options to scil_convert_sh_basis.py

Pull Request - State: closed - Opened by karanphil almost 2 years ago - 6 comments

#703 - Get version script

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

#702 - [BF] Error message - metrics stats in ROI

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

#701 - [BF] GPU tracking kernel cannot be called main

Pull Request - State: closed - Opened by CHrlS98 almost 2 years ago - 4 comments

#700 - Fix warnings in distortion correction

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

#699 - Make stopping criteria more obvious + more similar to dipy.

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

#698 - Investigating Dipy tracking??

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

#697 - Speeding the dev det tracking

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

#696 - (WIP) Adding script to apply transform to bvecs

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

#695 - [ENH] Upload frozen python requirements aside of release assets

Pull Request - State: closed - Opened by AlexVCaron almost 2 years ago - 3 comments

#694 - Update to hotdipy + fix load empty sft

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

#693 - Fixing warning always showing up.

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

#692 - Fix default sphere tracking

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

#691 - default sphere in scil_compute_local_tracking.py

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

#690 - Fix some deprecated import and fix some tests

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

#689 - Adding explanations to scil_compute_fodf_max_in_ventricles

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

#688 - Adding small_dims option to scil_compute_fodf_max_in_ventricles

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

#687 - fix seed mask empty

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

#686 - Switch to kdtree for uniformize --target

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

#685 - uint8 in compute_density when possible

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

#684 - Reactivate md5sum in fetcher

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

#683 - skip init in search_keyword.

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

#682 - Add python3.10-venv to packages to install

Pull Request - State: closed - Opened by CHrlS98 almost 2 years ago - 1 comment

#681 - Change version number

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

#680 - scilpy is broken on Python3.10

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

#679 - New script: Plot dipy sphere

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

#678 - [ENH] scilpy and python3.10

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

#677 - Parallelise remove_loops_and_sharp_turns

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

#676 - Fix multiprocess in dev tracking

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

#675 - (WIP) TRX Integration

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

#674 - Fix validate bids

Pull Request - State: closed - Opened by arnaudbore about 2 years ago - 9 comments

#673 - Adding PCA script for dimension reduction of metrics

Pull Request - State: closed - Opened by gagnonanthony about 2 years ago - 15 comments

#672 - Fixing uniform_coloring in scil_visualize_bunldes.py

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

#671 - Adding variance to scil_visualize_fodf

Pull Request - State: closed - Opened by karanphil about 2 years ago - 8 comments

#670 - [ENH] compute local tracking mask with no seed

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

#669 - [BF] bids_validate

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

#668 - Fixing unique in dev branch

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

#667 - [WIP] test

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

#666 - Python3 10 readme

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

#665 - Fix the unique len issue

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

#664 - [ENH] Mocks rollout and implementation of testing behaviors

Pull Request - State: open - Opened by AlexVCaron about 2 years ago - 23 comments
Labels: enhancement

#663 - [BF] Bids validate

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

#662 - Testing 3 10 upgrade

Pull Request - State: closed - Opened by frheault about 2 years ago - 24 comments

#661 - [ENH][BF] scil_validate_bids

Pull Request - State: closed - Opened by arnaudbore about 2 years ago - 27 comments

#660 - Exploration for python3.10 switch (WIP)

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

#659 - Unit tests for the new labels module

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

#658 - Module tractogram operations

Pull Request - State: closed - Opened by EmmaRenauld about 2 years ago - 11 comments

#657 - --no_empty in scil_remove invalid streamlines.py

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

#656 - Add back md5 sum checking in the data fetcher

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

#655 - Fix fetcher

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

#654 - BF validate_bids when full reverse

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

#653 - Bump pillow from 9.0.1 to 9.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 3 comments
Labels: dependencies

#652 - Bump pillow from 9.0.1 to 9.3.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 3 comments
Labels: dependencies

#651 - [BF] BG color as optional function argument

Pull Request - State: closed - Opened by CHrlS98 about 2 years ago - 3 comments

#650 - Fix total count

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

#649 - Fix logging for RBx (file handling)

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

#648 - Creating module 'labels'

Pull Request - State: closed - Opened by EmmaRenauld over 2 years ago - 7 comments

#647 - Fix logging across scilpy

Pull Request - State: closed - Opened by frheault over 2 years ago - 6 comments

#646 - Add check_bbox_false (only in scil_score_bundles)

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

#645 - [BF] validate BIDS

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

#644 - Add option to disable bbox checking in tractogram loading

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

#643 - Fix: names for overreach

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

#642 - Fix rare division by 0 in f1

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

#641 - Add check_bbox argument management

Pull Request - State: closed - Opened by EmmaRenauld over 2 years ago - 28 comments

#640 - Project streamlines from/to wm/gm

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

#639 - [ENH] POC : Use mocking to get faster execution of tests

Pull Request - State: closed - Opened by AlexVCaron over 2 years ago - 15 comments

#638 - Choose device option for GPU tracking

Issue - State: open - Opened by CHrlS98 over 2 years ago
Labels: Hackathon-Senior

#637 - Tensor format

Pull Request - State: closed - Opened by EmmaRenauld over 2 years ago - 9 comments

#636 - Coloring connectomics

Pull Request - State: closed - Opened by frheault over 2 years ago - 8 comments

#635 - Fix jenkins

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

#634 - Bug fix for scil_swap_gradient_axis

Pull Request - State: closed - Opened by CHrlS98 over 2 years ago - 3 comments

#633 - FIX: Add setuptools to jenkins config

Pull Request - State: closed - Opened by frheault over 2 years ago - 15 comments

#631 - ENH: unit test PoC

Pull Request - State: closed - Opened by AntoineTheb over 2 years ago - 7 comments
Labels: enhancement

#630 - Added OLO to reorder_connectivity

Pull Request - State: closed - Opened by frheault over 2 years ago - 4 comments

#627 - [ENH] Add multiple ID to filter tractogram with atlas

Pull Request - State: closed - Opened by arnaudbore over 2 years ago - 12 comments

#626 - Gradient sampling ajustment

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

#623 - [ENH] Extract gradient scheme from eddy output - for tractoflow

Pull Request - State: closed - Opened by arnaudbore over 2 years ago - 12 comments

#622 - Creating new script to score tractogram that is already segmented.

Pull Request - State: closed - Opened by EmmaRenauld over 2 years ago - 16 comments

#620 - Doubled code

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

#619 - [BF] Update bundle metrics - handle NaN

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

#618 - scil_compute_bundle_voxel_label_map can output tractogram with 1 point streamline

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

#617 - Bump joblib from 1.1.0 to 1.2.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 6 comments
Labels: dependencies

#616 - Add a function to verify compatibility

Pull Request - State: closed - Opened by arnaudbore over 2 years ago - 9 comments

#610 - [WIP] update numpy - bot

Pull Request - State: closed - Opened by arnaudbore over 2 years ago - 5 comments

#609 - Update prepare eddy

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

#606 - Script swap_gradient_axis.py left an axis to 0

Issue - State: closed - Opened by gabe1496 over 2 years ago

#605 - Reorg of tractogram filtering functions

Issue - State: closed - Opened by grahamlittlephd over 2 years ago - 5 comments

#602 - scil_search_keywords does not work anymore

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

#596 - scil_apply_transform_to_image.py doesn't change bvecs

Issue - State: closed - Opened by karanphil over 2 years ago - 3 comments

#591 - [ENH] Validate bids

Pull Request - State: closed - Opened by arnaudbore over 2 years ago - 15 comments

GitHub / scilus/scilpy issues and pull requests