Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / cohenlabUNC/clpipe issues and pull requests

#440 - Project_setup error

Issue - State: open - Opened by mackenziemitchell 7 months ago

#438 - 1.9.1.7 hotfix

Pull Request - State: closed - Opened by yuvrajjain2003 7 months ago

#437 - 1.9.1.5 hotfix

Pull Request - State: closed - Opened by yuvrajjain2003 9 months ago
Labels: bug, documentation

#434 - GLM Parent Config Reference Issue

Issue - State: open - Opened by wasciutto 12 months ago

#433 - Release 1.9.1

Pull Request - State: closed - Opened by wasciutto 12 months ago

#432 - output niftis in clpipe/1.9.0 postprocessing are in Talairach space

Issue - State: closed - Opened by adcascone 12 months ago - 1 comment

#430 - 1.9.0.8 hotfix

Pull Request - State: closed - Opened by wasciutto about 1 year ago

#429 - 1.9.0.7 hotfix

Pull Request - State: closed - Opened by wasciutto about 1 year ago

#427 - Tolerate file name spaces

Pull Request - State: closed - Opened by yuvrajjain2003 about 1 year ago

#426 - sphere_radius name throwing bug

Issue - State: closed - Opened by wasciutto about 1 year ago

#424 - 1.9.0.6 hotfix

Pull Request - State: closed - Opened by wasciutto about 1 year ago

#423 - bids validate logs going to wrong place and None in logs

Issue - State: closed - Opened by wasciutto about 1 year ago

#422 - Bids indexing

Pull Request - State: closed - Opened by yuvrajjain2003 about 1 year ago

#420 - Refresh Index Failing Even with Correct Permissions

Issue - State: closed - Opened by wasciutto about 1 year ago - 1 comment
Labels: postprocess

#419 - 1.9.0.4 hotfix

Pull Request - State: closed - Opened by wasciutto about 1 year ago

#418 - Update to Python 3.8 to Use Pybids 16.0

Issue - State: open - Opened by wasciutto about 1 year ago

#417 - heudiconv: logs save to wrong place (point of calling)

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

#416 - preprocess gives wrong log value

Issue - State: closed - Opened by wasciutto about 1 year ago

#415 - Have config get_default Work Off Project Directory

Issue - State: open - Opened by wasciutto about 1 year ago
Labels: config

#414 - Configuration Defaults Fix

Issue - State: closed - Opened by wasciutto about 1 year ago
Labels: config

#413 - Multiple scrubbing

Pull Request - State: closed - Opened by yuvrajjain2003 about 1 year ago - 1 comment

#412 - dcm2bids v3+ incompatible with fMRIprep <= v23

Issue - State: open - Opened by wasciutto about 1 year ago
Labels: bug, dependencies

#411 - Modality becomes datatype in new BIDS standard

Issue - State: open - Opened by wasciutto about 1 year ago
Labels: convert2bids

#410 - Wrong Path in Docs

Issue - State: closed - Opened by wasciutto about 1 year ago
Labels: documentation

#409 - Create Class-Based Configuration for Batch Options

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: config

#408 - 1.8.1.1 hotfix

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

#407 - Create test for postprocess_image

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: postprocess2, test

#406 - Create fixture for BIDS dir

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: postprocess2, test

#405 - Scrubbing/Trimming Should Also Modify Mixing File

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: postprocess2

#404 - Set permissions of files/folders created to always be open for group write

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: setup

#403 - 1.9.0 release

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

#402 - Support Wildcard Selection within Scrubbing Step

Issue - State: closed - Opened by wasciutto over 1 year ago - 1 comment
Labels: postprocess2

#401 - Figure out how to index only fMRIPrep func folder with patterns

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: postprocess2

#400 - Add Jess's Variation of ROI Extraction

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: roi

#399 - Group Batch Log Outputs

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: logging

#398 - Remove Redundancy From Workflow Test Code

Issue - State: closed - Opened by wasciutto over 1 year ago - 2 comments
Labels: test

#397 - Confound Regression not Working Correctly with Scrubbed Confounds

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: bug, postprocess2

#396 - Remove use of fMRIPrep Masks as default due to Poor Quality

Issue - State: open - Opened by wasciutto over 1 year ago - 1 comment
Labels: postprocess2

#395 - Slow Indexing of fMRIPrep Directory

Issue - State: closed - Opened by wasciutto over 1 year ago - 1 comment
Labels: postprocess2

#393 - Release 1.8.1

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

#392 - Develop

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

#391 - Add record of project_setup command

Issue - State: closed - Opened by mackenziemitchell over 1 year ago - 2 comments
Labels: logging

#390 - Enforce Heudiconv < v13.0.0

Issue - State: closed - Opened by wasciutto over 1 year ago - 2 comments
Labels: dependencies

#389 - Wf 3dt project

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

#388 - 1.8.0.6 hotfix

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

#387 - Support Multiple Column Selection for Scrubbing

Issue - State: closed - Opened by wasciutto over 1 year ago - 4 comments
Labels: postprocess2, 1.9 Req

#386 - Document Postprocess2 Step Implementations

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: documentation, postprocess2, medium

#385 - Support Wildcarding For Confound Column Selection

Issue - State: closed - Opened by wasciutto over 1 year ago - 3 comments
Labels: postprocess2, medium

#384 - Document Scrubbing Step

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: documentation, postprocess2, 1.8.1 Req, small

#383 - 1.8.0.5 hotfix

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

#382 - Option overlap_ok not included in configuration

Issue - State: closed - Opened by wasciutto over 1 year ago - 1 comment
Labels: good first issue, roi

#381 - Figure out how to differentiate regressed vs. glm confounds

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: postprocess2, small

#380 - Confounds settings do not override defaults

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: bug, postprocess2, 1.8.1 Req, small

#379 - Extraction won't work with mask due to 'empty spheres'

Issue - State: closed - Opened by wasciutto over 1 year ago - 4 comments
Labels: question, roi

#375 - Throw Better Error when Noise Components File Empty

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: good first issue, postprocess2

#374 - Include nipype options by default

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: postprocess2

#373 - Var referenced before assignment

Issue - State: closed - Opened by wasciutto over 1 year ago - 2 comments
Labels: bug, postprocess2, 1.8.1 Req, medium

#372 - Add ability to consume non-zipped nii files

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: postprocess2

#371 - 1.8.0.4 hotfix

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

#367 - Add 3dTProject Implementation as Alternate Filtering Step

Issue - State: closed - Opened by wasciutto over 1 year ago - 1 comment
Labels: postprocess2, 1.8.1 Req, large

#365 - preprocess: ignores value given for log file in config file

Issue - State: closed - Opened by wasciutto over 1 year ago - 1 comment
Labels: bug, preprocess

#364 - aroma regress fslregfilt: Add ability to mask

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: postprocess2

#362 - Use New Config File System in GLM Commands.

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: new config

#361 - Use New Config System in Postprocessing & ROI commands

Issue - State: closed - Opened by wasciutto over 1 year ago
Labels: new config

#360 - Use New Config System in Preprocessing Line

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: new config

#359 - Add Config File Updater to CLI menu

Issue - State: closed - Opened by wasciutto over 1 year ago - 1 comment
Labels: new config, CLI, 1.9 Req

#358 - Removed deprecated bids and dicom sub-menus by v1.9.0

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: 2.0 Req, CLI

#356 - Level-dependent Console Log Labeling

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: logging

#336 - Raise error if .json file is not a clpipe configuration file

Issue - State: open - Opened by wasciutto over 1 year ago
Labels: new config

#325 - Deprecate all non-clpipe menu commands

Issue - State: open - Opened by wasciutto over 1 year ago

#323 - fmri_process_check: add support for postproc2

Issue - State: open - Opened by wasciutto over 1 year ago - 1 comment
Labels: quick

#314 - Provide a default README file

Issue - State: open - Opened by wasciutto almost 2 years ago
Labels: project_setup

#298 - Improve Heudiconv Error Message When No Subjects Found

Issue - State: open - Opened by wasciutto almost 2 years ago
Labels: convert2bids

#288 - Write a Simple Contribution Guide

Issue - State: closed - Opened by wasciutto almost 2 years ago - 1 comment
Labels: documentation

#277 - Investigate double usage of BIDS directory in Bids conversion and fmriprep process

Issue - State: open - Opened by wasciutto about 2 years ago
Labels: convert2bids

#276 - Add "longitudinal" flag to DCM2BIDS Configuration File

Issue - State: open - Opened by wasciutto about 2 years ago
Labels: good first issue

#274 - Use Sphinx to Autogenerate API Documentation

Issue - State: open - Opened by wasciutto about 2 years ago
Labels: documentation

#261 - Add command to setup either dcm2bids or heudiconv

Issue - State: open - Opened by wasciutto about 2 years ago - 1 comment
Labels: convert2bids

#246 - Log the processing steps being used

Issue - State: open - Opened by wasciutto over 2 years ago
Labels: good first issue, quick, postprocess2, UX

#241 - Provide 3dTProject Implementation of Temporal Filtering

Issue - State: closed - Opened by wasciutto over 2 years ago - 2 comments
Labels: enhancement, postprocess2

#238 - Provide fmri.pipeline Wrapper Command

Issue - State: open - Opened by wasciutto over 2 years ago - 1 comment

#237 - Combine confound outliers summary with postproc2

Issue - State: open - Opened by wasciutto over 2 years ago

#235 - Use Sphinx to Update Configuration File Documentation

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

#231 - Remove empty folder creation from project-setup

Issue - State: open - Opened by wasciutto over 2 years ago
Labels: request

#230 - Save nipype crash logs to sub-directory

Issue - State: open - Opened by wasciutto over 2 years ago
Labels: quick, postprocess2, UX

#226 - List Available Processing Streams Option

Issue - State: open - Opened by wasciutto over 2 years ago - 1 comment
Labels: good first issue, postprocess2, UX

#225 - Show Available Algorithms

Issue - State: open - Opened by wasciutto over 2 years ago
Labels: good first issue, postprocess2, UX

#213 - Do Not Pass Config Dict to Business Logic

Issue - State: open - Opened by wasciutto over 2 years ago - 1 comment
Labels: postprocess2

#199 - ROI Extraction - Add Radius Specification to ROI Config

Issue - State: open - Opened by wasciutto over 2 years ago - 1 comment

#169 - Allow Working Directories to be Cleared

Issue - State: open - Opened by wasciutto almost 3 years ago - 1 comment
Labels: postprocess2, small

#161 - Pass pybids Index Reference to Jobs Through Config Instead of BIDS directory path.

Issue - State: open - Opened by wasciutto almost 3 years ago
Labels: postprocess2

#133 - Postprocessing documentation request

Issue - State: closed - Opened by macmitch almost 4 years ago
Labels: documentation

#102 - Add drop_tps option to config file

Issue - State: open - Opened by trh3 almost 5 years ago

#100 - Merge fixes into dev

Pull Request - State: closed - Opened by trh3 almost 5 years ago