Ecosyste.ms: Issues

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GitHub / scilus/scilpy issues and pull requests

#1134 - [FAKE PR] Do not ignore legacy

Pull Request - State: open - Opened by EmmaRenauld 21 days ago - 1 comment

#1133 - Add test for volume_metrics

Pull Request - State: open - Opened by EmmaRenauld 21 days ago - 1 comment

#1132 - Working test of SFS in Python3.12

Pull Request - State: open - Opened by frheault 22 days ago - 1 comment

#1131 - Installation guidelines improvements

Issue - State: open - Opened by mdesco 23 days ago

#1130 - fix colorbar with nb_value

Pull Request - State: open - Opened by Thierry56511 26 days ago - 1 comment

#1129 - dwi_prepare_eddy_command options

Issue - State: closed - Opened by EliseCos 26 days ago - 1 comment

#1128 - Problem running some scripts with new release

Issue - State: open - Opened by mdesco 27 days ago

#1127 - No test file for new script

Issue - State: open - Opened by EmmaRenauld 28 days ago

#1126 - Small fix (issue 1123)

Pull Request - State: closed - Opened by EmmaRenauld 28 days ago - 1 comment

#1125 - Support .tck for commit

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

#1124 - scil_tractogram_commit needs a --reference to work with .tck input

Issue - State: closed - Opened by mdesco 28 days ago - 1 comment

#1123 - scil_tractogram_segment_connections_from_labels.py bug with --out_dir

Issue - State: closed - Opened by mdesco 29 days ago - 2 comments

#1121 - bids_validate func get_data -> changed clean: Boolean definition from…

Pull Request - State: open - Opened by Desk3505 about 1 month ago - 1 comment

#1120 - update scilpy: remove old stuff now in dipy

Issue - State: open - Opened by arnaudbore about 1 month ago - 1 comment

#1119 - [ENH] Add an option to cut streamlines

Pull Request - State: open - Opened by arnaudbore about 1 month ago - 3 comments

#1118 - [ENH] Add positionnal arguments

Pull Request - State: closed - Opened by arnaudbore about 1 month ago - 2 comments

#1117 - [ENH] Allow extra option for topup and eddy

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

#1115 - [BF] NODDI map catch error

Pull Request - State: closed - Opened by arnaudbore about 1 month ago - 2 comments

#1114 - update to dipy 1.10

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

#1113 - Fixing the skip_b0_check function

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

#1112 - Fibertube Density

Pull Request - State: closed - Opened by VincentBeaud 2 months ago - 3 comments

#1111 - [New feature] Topup configuration selection

Issue - State: open - Opened by AlexVCaron 2 months ago
Labels: enhancement

#1110 - Add script to validate gradient tables

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

#1109 - Fix merge queue

Pull Request - State: closed - Opened by AlexVCaron 2 months ago - 1 comment

#1108 - Argument skip_b0_check always overwrites with minimum

Issue - State: closed - Opened by karanphil 2 months ago - 2 comments

#1107 - DOC - fixed updated script name

Pull Request - State: closed - Opened by gabknight 2 months ago - 1 comment

#1106 - Add Scilpy version - part 2

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

#1105 - ENH: remove `sft._data` usage part 1 - tractogram coloring scripts + more

Pull Request - State: open - Opened by AntoineTheb 2 months ago - 4 comments

#1104 - Using fixtures in tests

Issue - State: open - Opened by levje 2 months ago

#1103 - DOC - renamed the uncompress fct to streamlines_to_voxel_coordinates

Pull Request - State: open - Opened by gabknight 2 months ago - 3 comments

#1102 - [WIP] Unit tests connectivity

Pull Request - State: open - Opened by EmmaRenauld 2 months ago - 1 comment

#1101 - Cythonization warnings

Pull Request - State: closed - Opened by CHrlS98 2 months ago - 2 comments

#1100 - Add Scilpy version - part 1

Pull Request - State: closed - Opened by zinelya 2 months ago - 1 comment

#1099 - Final connectivity scripts PR

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

#1098 - BF - fixed voxel bundary conditions in uncompress streamlines

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

#1097 - Update script scil_viz_gradients_screenshot

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

#1096 - Change Crop Volume BBOX for a json

Pull Request - State: open - Opened by AlexVCaron 2 months ago - 2 comments

#1095 - IO fetcher

Issue - State: open - Opened by arnaudbore 2 months ago
Labels: Hackathon-Senior

#1094 - Fixing bug in gradients_generate_sampling

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

#1093 - [WIP] Script validate gradient table

Pull Request - State: closed - Opened by VincentBeaud 2 months ago - 4 comments

#1092 - Fix the hdf5 error when dpp are present

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

#1091 - Update tests - parallele

Pull Request - State: open - Opened by arnaudbore 2 months ago

#1090 - FIX: Filter streamlines by length, use the "save rejection" argument.

Pull Request - State: closed - Opened by levje 2 months ago - 1 comment

#1089 - FIX: Division by 0 in `scil_dti_metrics`

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

#1088 - Move plot residuals into viz - plot

Pull Request - State: closed - Opened by elyz081 2 months ago - 2 comments

#1087 - Cleaning the connectivity pairwise agreement script

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

#1086 - Adding support for list of lists of paths in assert_inputs_exist

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

#1085 - Fix Fury upcoming deprecation call

Pull Request - State: closed - Opened by AlexVCaron 2 months ago - 1 comment

#1084 - Condense distance matrix that was not. Pep8 + test pass

Pull Request - State: closed - Opened by VincentBeaud 2 months ago - 4 comments

#1083 - Adding ref to scil_freewater_maps

Pull Request - State: closed - Opened by karanphil 2 months ago

#1082 - Switch to loops simple connectivity

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

#1080 - Add test single shell NODDI

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

#1079 - [DOC] Add documentation for grid_intersections

Pull Request - State: closed - Opened by CHrlS98 2 months ago - 5 comments

#1078 - Avoid scalar with dim > 0 by squeezing. Passes test and pep8 no warning.

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

#1077 - BF for asymmetric peaks

Pull Request - State: closed - Opened by CHrlS98 2 months ago - 2 comments

#1076 - [FIX]: Return rejected streamlines with empty sft

Pull Request - State: closed - Opened by levje 2 months ago - 3 comments

#1075 - New Endpoint Scoring - Charles' suggestions

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

#1074 - Add script to validate a gradient table

Issue - State: open - Opened by arnaudbore 2 months ago
Labels: Hackathon-Senior

#1073 - Filter streamline by length failure with sft with no streamline

Issue - State: closed - Opened by levje 2 months ago
Labels: Hackathon-Senior

#1072 - scil_viz_fodf.py can't visulize peaks.

Issue - State: closed - Opened by gaunny 2 months ago - 3 comments

#1070 - Add Fibertube_tracking.rst to the read-the-docs

Pull Request - State: closed - Opened by CHrlS98 3 months ago - 1 comment

#1069 - Tracking local custom seeds

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

#1068 - RF - Input to volume stats scripts

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

#1067 - Function assert_inputs_exist does not work with a list of lists

Issue - State: closed - Opened by karanphil 3 months ago
Labels: Hackathon-Senior

#1066 - Script dps math

Pull Request - State: closed - Opened by VincentBeaud 3 months ago - 4 comments

#1065 - ENH: add interpolation to `scil_volume_apply_transform`

Pull Request - State: closed - Opened by AntoineTheb 3 months ago - 1 comment

#1064 - Fibertube tracking - New endpoint scoring

Pull Request - State: closed - Opened by VincentBeaud 3 months ago - 2 comments

#1063 - Next connectivity scripts

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

#1062 - Numpy deprecation warning

Issue - State: closed - Opened by EmmaRenauld 3 months ago - 1 comment
Labels: Hackathon-Senior

#1061 - Invalid help

Issue - State: open - Opened by EmmaRenauld 3 months ago - 1 comment
Labels: Hackathon-Senior

#1060 - Todo: Fix scipy warning

Issue - State: closed - Opened by EmmaRenauld 3 months ago
Labels: Hackathon-Senior

#1059 - [VIS] Fury upcoming deprecated call

Issue - State: closed - Opened by EmmaRenauld 3 months ago
Labels: Hackathon-Senior

#1058 - toDo: improve loop in my script

Issue - State: closed - Opened by EmmaRenauld 3 months ago
Labels: Hackathon-Senior

#1056 - Fix doc

Pull Request - State: closed - Opened by EmmaRenauld 3 months ago - 1 comment

#1054 - Division by 0

Issue - State: open - Opened by EmmaRenauld 3 months ago - 3 comments
Labels: Hackathon-Senior

#1052 - [BF] Tractogram filter by multiples ROIs - Crash

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

#1049 - New scripts suggestions or new features

Issue - State: open - Opened by arnaudbore 3 months ago - 1 comment
Labels: Hackathon-Senior

#1045 - Create new script compute_simple_matrix

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

#1044 - Possible upcoming issue with panda

Issue - State: closed - Opened by EmmaRenauld 4 months ago - 1 comment

#1039 - harmonzie labels for longitudinal lesions - WIP

Pull Request - State: open - Opened by frheault 4 months ago - 5 comments

#1038 - Add header info when saving into nifti

Issue - State: open - Opened by arnaudbore 4 months ago - 1 comment
Labels: Hackathon - Junior

#1035 - BundleSeg exploration viewer for filtering

Pull Request - State: open - Opened by frheault 4 months ago - 3 comments

#1034 - Hyperplane update

Pull Request - State: open - Opened by frheault 5 months ago - 2 comments

#1029 - freewater estimation

Issue - State: open - Opened by raywell627 5 months ago - 1 comment

#1028 - [WIP] Fix tests

Pull Request - State: open - Opened by arnaudbore 5 months ago - 1 comment

#1027 - Tractograms: more unit tests

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

#1026 - Nawm generation based on distance map

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

#1025 - Error while building scilpy from source

Issue - State: open - Opened by zhitao-guo 6 months ago

#1024 - Update test data key to 'tractograms.zip' instead of 'atlas.zip'

Pull Request - State: open - Opened by elyz081 6 months ago - 3 comments

#1023 - Distance map

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

#1022 - [ENH] Add mrds scripts part 2

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

#1021 - [ENH] Add mrds scripts part 1

Pull Request - State: open - Opened by arnaudbore 6 months ago - 2 comments

#1020 - Modify lesions_info to support labels instead of mask

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

#1019 - ENH: Pad or crop volume using `scil_volume_reshape.py`

Pull Request - State: open - Opened by AntoineTheb 7 months ago - 4 comments
Labels: enhancement

#1018 - Removing unused argument in scil_bundle_fixel_analysis.py

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

#1017 - WIP: fODF interpolation (help needed)

Pull Request - State: open - Opened by AntoineTheb 7 months ago - 5 comments
Labels: bug, enhancement