yeatmanlab/pyAFQ issues and pull requests

#1164 - Warning: "Failure to converge" error occurring when running pyAFQ

Issue - State: open - Opened by dzweben 16 days ago

#1163 - Include binary stop masks

Issue - State: open - Opened by kellychang4 25 days ago

#1162 - Questions about a custom bundle

Issue - State: open - Opened by htakemur 26 days ago - 3 comments

#1161 - [FIX] Do not assume VOX space in clean bundles function

Pull Request - State: closed - Opened by 36000 about 1 month ago

#1160 - [FIX] bug in finding ROI from freesurfer using pybids

Pull Request - State: closed - Opened by 36000 about 1 month ago - 2 comments

#1159 - ValueError: Expected subject IDs to match

Issue - State: closed - Opened by teresamg about 1 month ago - 3 comments

#1158 - [FIX] Fix bug in filtering by bval, where b0 calculation used mismatched dwi and gtab

Pull Request - State: closed - Opened by 36000 about 1 month ago

#1157 - Update GPU tracking to use probabilistic and PTT options

Pull Request - State: open - Opened by 36000 about 1 month ago - 2 comments

#1156 - Issues with setting max_bval

Issue - State: closed - Opened by audreycluo about 1 month ago - 5 comments

#1155 - Question about a custom bundle

Issue - State: closed - Opened by htakemur about 1 month ago - 9 comments

#1154 - Scalar names that are more BIDS compliant

Issue - State: open - Opened by arokem about 1 month ago

#1153 - allow identity mapping from CLI

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

#1152 - [ENH] Auto detect B-vector issues

Issue - State: open - Opened by 36000 about 2 months ago - 1 comment

#1151 - Update bundledict.rst

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

#1150 - Update kwargs.rst

Pull Request - State: closed - Opened by chiuhoward about 2 months ago

#1149 - afqbrowser-asemble not working: (error): "nodes inconsistent length"

Issue - State: open - Opened by dzweben 2 months ago - 1 comment

#1148 - when running pyAFQ: "Failed to export warped b0" error

Issue - State: closed - Opened by dzweben 2 months ago - 1 comment

#1147 - Test with python 3.12

Pull Request - State: open - Opened by arokem 3 months ago - 1 comment

#1146 - Newest Version of Python isn't working for pip install pyAFQ

Issue - State: open - Opened by dzweben 3 months ago - 1 comment

#1145 - Fixes small typo in plot_001_afq_api.py

Pull Request - State: closed - Opened by arokem 4 months ago

#1144 - [ENH] add system for finding bundles relative to other bundles

Pull Request - State: open - Opened by 36000 4 months ago - 2 comments

#1143 - [FIX] Update fetch.py with pediatric ARC ROI mapping

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

#1142 - [FIX] Remove unused parameter, filter_by_endpoints

Pull Request - State: closed - Opened by 36000 4 months ago - 1 comment

#1141 - Adds engine:serial default

Pull Request - State: closed - Opened by teresamg 4 months ago - 6 comments

#1140 - Test against the numpy 2.0 release candidate.

Pull Request - State: open - Opened by arokem 5 months ago

#1139 - Check bvals on dki

Pull Request - State: closed - Opened by 36000 5 months ago

#1138 - [FIX] different CST ROI 2 for L/R

Pull Request - State: closed - Opened by 36000 5 months ago - 4 comments

#1137 - Distance transform

Issue - State: open - Opened by arokem 5 months ago

#1136 - Streamlines task in parallel using ray

Pull Request - State: closed - Opened by asagilmore 5 months ago - 9 comments

#1135 - [DOC] Update kwargs.rst

Pull Request - State: closed - Opened by chiuhoward 5 months ago

#1134 - WIP: Generates default dataset_description.json if not present

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

#1133 - WIP: Bval error check

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

#1132 - [REF] Refactor segmentation code into many files and pimms system

Pull Request - State: closed - Opened by 36000 5 months ago - 5 comments

#1131 - [DOC] Update baby_afq.py

Pull Request - State: closed - Opened by chiuhoward 6 months ago

#1130 - Make altair required

Pull Request - State: closed - Opened by 36000 6 months ago - 1 comment

#1129 - [ENH] Added RUMBA-SD to data.py

Pull Request - State: closed - Opened by chiuhoward 6 months ago - 10 comments

#1128 - [ENH, WIP] More tracking options

Pull Request - State: open - Opened by 36000 6 months ago - 2 comments

#1127 - [ENH] expose FA thresh param for autoresponse ssst for csd

Pull Request - State: closed - Opened by 36000 6 months ago

#1126 - [DOC] Some improvements to the documentation based on conversations during the hackathon

Pull Request - State: closed - Opened by 36000 6 months ago - 1 comment

#1125 - Improve performance on large datasets by using bids2table

Issue - State: open - Opened by arokem 6 months ago

#1124 - Adds ParallelGroupAFQ

Pull Request - State: closed - Opened by teresamg 6 months ago - 13 comments

#1123 - [ENH] small change to viz utils panel code

Pull Request - State: closed - Opened by 36000 6 months ago

#1122 - [WIP] GAM Tract Profile Tutorial

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

#1121 - [ENH] add mean signal diffusion kurtosis model

Pull Request - State: closed - Opened by 36000 6 months ago

#1120 - [DOC] add bundle orientation explanation

Pull Request - State: closed - Opened by 36000 6 months ago

#1119 - Simple way to increase pyAFQ flexibility

Issue - State: open - Opened by 36000 6 months ago

#1118 - [ENH] make source field relative in json sidecars

Pull Request - State: closed - Opened by 36000 6 months ago - 1 comment

#1117 - [ENH] add more information from bundle dict into jsons

Pull Request - State: closed - Opened by 36000 6 months ago - 1 comment

#1116 - [FIX] fix bundle colors

Pull Request - State: closed - Opened by 36000 7 months ago - 1 comment

#1115 - Fix gpu tracking

Pull Request - State: closed - Opened by 36000 7 months ago

#1114 - HTML tract colors got scrambled with renaming of tracts?

Issue - State: closed - Opened by arokem 7 months ago - 1 comment

#1113 - [DOC] try to reproduce and fix nightly test

Pull Request - State: closed - Opened by 36000 7 months ago - 1 comment

#1112 - [WIP, ENH] begin integrating fastsurfer

Pull Request - State: open - Opened by 36000 7 months ago

#1111 - [FIX] Set parc/vof cleaning params to default

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

#1110 - Save Bundle info to individual bundles' JSON file

Issue - State: closed - Opened by 36000 8 months ago

#1109 - Move s3 BIDS to separate repo

Pull Request - State: closed - Opened by 36000 8 months ago - 1 comment

#1108 - [DOC] make altair example

Pull Request - State: closed - Opened by 36000 8 months ago - 1 comment

#1107 - Add conversion dictionary for old acronyms

Pull Request - State: closed - Opened by 36000 8 months ago - 1 comment

#1106 - Revert #1086?

Issue - State: open - Opened by arokem 8 months ago - 7 comments

#1105 - [ENH] allow random seeds in gpu tracking

Pull Request - State: closed - Opened by 36000 8 months ago - 1 comment

#1104 - [FIX] force upgraded joblib

Pull Request - State: closed - Opened by 36000 8 months ago

#1103 - [ENH/FIX] Smarter file finding

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

#1102 - Upgrade python versions supported, and drop 3.8.

Pull Request - State: closed - Opened by arokem 8 months ago - 1 comment

#1101 - Make the altair code a little more flexible

Pull Request - State: closed - Opened by 36000 8 months ago - 1 comment

#1100 - [ENH] Make the cleaning easier to interact with

Pull Request - State: closed - Opened by 36000 8 months ago

#1099 - [ENH] Order all bundles according to LPI+

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

#1098 - Paths should be relative

Issue - State: closed - Opened by 36000 8 months ago

#1097 - [ENH] add anisotropic kurtosis, make dki default?

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

#1096 - [ENH] Seeding on the white matter-gray mattter interface

Pull Request - State: open - Opened by 36000 8 months ago - 2 comments

#1095 - [FIX] update this nightly test

Pull Request - State: closed - Opened by 36000 8 months ago

#1094 - [ENH] Some segmentation speed-ups

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

#1093 - Reorder non-callosal ROIs

Issue - State: closed - Opened by arokem 9 months ago

#1092 - Reorder callosal ROIs

Issue - State: closed - Opened by arokem 9 months ago

#1091 - [FIX] Fix GPU Tractography

Pull Request - State: closed - Opened by 36000 9 months ago - 7 comments

#1090 - Link from website documentation to the release notes on GitHub

Issue - State: open - Opened by arokem 9 months ago

#1089 - Use only the lowest shell in calculation of the CSD response function.

Pull Request - State: closed - Opened by arokem 9 months ago - 1 comment

#1088 - [FIX] correct typo in baby bundle dict OR

Pull Request - State: closed - Opened by 36000 9 months ago - 2 comments

#1087 - [ENH] simplify verbose tracking

Pull Request - State: closed - Opened by 36000 9 months ago - 1 comment

#1086 - [ENH] Begin removing confusing abbreviations

Pull Request - State: closed - Opened by 36000 9 months ago - 5 comments

#1085 - A couple of small doc fixes

Pull Request - State: closed - Opened by arokem 9 months ago - 1 comment

#1084 - [ENH] more little tweaks to the AFQ viz utils panelfigure class

Pull Request - State: closed - Opened by 36000 9 months ago - 3 comments

#1083 - DOC: Small fixes to the visualization example.

Pull Request - State: closed - Opened by arokem 9 months ago - 1 comment

#1082 - Remove pyafq_cli.json

Issue - State: closed - Opened by arokem 9 months ago - 1 comment

#1081 - Interactions with QSIrecon output and BIDS specification

Issue - State: open - Opened by dkp 9 months ago - 9 comments

#1080 - Update fury

Pull Request - State: closed - Opened by 36000 9 months ago - 1 comment

#1079 - Possible upgrade to fury 0.9.0 in future release?

Issue - State: closed - Opened by chiuhoward 10 months ago - 1 comment

#1078 - [WIP/ENH] add AR from endpoint ROIs

Pull Request - State: closed - Opened by 36000 10 months ago - 2 comments

#1077 - Typos in Visualizing AFQ derivatives tutorial

Issue - State: closed - Opened by chiuhoward 10 months ago

#1076 - Update grant funding

Pull Request - State: closed - Opened by arokem 10 months ago - 3 comments

#1075 - Using the default bundle definition raises warnings

Issue - State: open - Opened by arokem 10 months ago - 3 comments

#1074 - [FIX] Add exclusion ROI to IFOF

Pull Request - State: closed - Opened by 36000 10 months ago - 4 comments

#1073 - Adds an example to plot stages of tractometry.

Pull Request - State: closed - Opened by arokem 10 months ago - 14 comments

#1072 - Changed order of probability map

Pull Request - State: closed - Opened by zikaste 10 months ago

GitHub / yeatmanlab/pyAFQ issues and pull requests