PennLINC/aslprep issues and pull requests

#342 - --skip-bids-validation not skipping all bids validation

Issue - State: open - Opened by caugolm about 1 year ago - 5 comments
Labels: bug

#341 - Allow `init_asl_t1_trans_wf` to accept flexible set of native-space inputs to warp

Issue - State: closed - Opened by tsalo about 1 year ago - 2 comments
Labels: refactor

#340 - Allow `init_asl_std_trans_wf` to accept flexible set of native-space inputs to warp

Issue - State: closed - Opened by tsalo about 1 year ago - 2 comments
Labels: refactor

#339 - Add 0.5.x release notes to changelog

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: documentation

#338 - Remove sdcflows and model ASLPrep on fMRIPrep/next

Pull Request - State: closed - Opened by tsalo about 1 year ago - 19 comments
Labels: enhancement, breaking-change, nipreps

#337 - Raise error if no M0 volume(s)/estimate available and background suppression is enabled

Pull Request - State: closed - Opened by tsalo about 1 year ago
Labels: bug

#336 - Support direct ASL-to-template or CBF-to-template normalization

Issue - State: open - Opened by tsalo about 1 year ago
Labels: enhancement

#335 - Should we prevent no-M0 processing when background suppression is enabled

Issue - State: closed - Opened by tsalo about 1 year ago
Labels: bug

#334 - Replace AtlasPack 0.0.5 atlases with AtlasPack 0.1.0 atlases

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: enhancement, breaking-change

#333 - Pin scipy version to 1.10.1

Pull Request - State: closed - Opened by tsalo about 1 year ago
Labels: bug

#332 - Ensure data are in LAS+ early on in pipeline

Issue - State: open - Opened by tsalo about 1 year ago
Labels: enhancement

#331 - Write out dataset_description.json

Issue - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: enhancement, wontfix

#330 - Add AtlasPack atlases

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: enhancement, breaking-change

#329 - Document M0 use in reports

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: documentation

#328 - Fix `BolusCutOffTechnique` typo

Pull Request - State: closed - Opened by tsalo about 1 year ago
Labels: bug

#327 - `BolusCutOffTechnique` misspelled as `BolusCutOffDelayTechnique`

Issue - State: closed - Opened by tsalo about 1 year ago
Labels: bug

#326 - Add project roadmap to the repository

Issue - State: open - Opened by tsalo about 1 year ago - 2 comments
Labels: documentation, maintenance

#325 - Remove unnecessary dependencies

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: maintenance

#324 - Document M0 situation in report

Issue - State: closed - Opened by tsalo about 1 year ago
Labels: documentation, enhancement

#323 - Make M0 TR optional for BASIL

Pull Request - State: closed - Opened by tsalo about 1 year ago - 2 comments
Labels: bug

#322 - Support `--basil` with absent or estimate M0 scans

Issue - State: closed - Opened by tsalo about 1 year ago
Labels: enhancement

#321 - Patch regmotoasl again

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: bug

#320 - Patch regmotoasl

Pull Request - State: closed - Opened by tsalo about 1 year ago - 1 comment
Labels: bug, documentation

#319 - Workflow with separate M0 fails at registration step

Issue - State: closed - Opened by chidiugonna about 1 year ago - 8 comments
Labels: bug

#318 - Start centralizing docstring entries

Pull Request - State: open - Opened by tsalo over 1 year ago
Labels: refactor

#317 - Write out QC metadata

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#316 - Fix CombineMotionParameters to support single-volume volume types

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: bug

#315 - Remove M0 metadata from multi-PLD GE metadata dictionary

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: bug

#314 - Multi-PLD is not supported for GE data

Issue - State: closed - Opened by tsalo over 1 year ago - 8 comments
Labels: bug

#313 - Add force-ge and force-no-ge parameters

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#312 - Fix the Docker image

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug

#311 - ASLPrep is not installed in Docker image after packaging refactor

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: bug

#310 - ASLPrep hangs when changing dseg datatype

Issue - State: closed - Opened by Luoyu-Wang over 1 year ago - 29 comments
Labels: bug

#309 - Fix Docker build steps

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: maintenance

#308 - Docker build step fails

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: bug, maintenance

#307 - Fix deployment config

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug, ignore-for-release, maintenance

#306 - Add top-level sidecar file for PennLINC QC file

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#305 - Fix deployment configuration

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug, ignore-for-release

#304 - Update contributor lists

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: ignore-for-release, maintenance

#303 - Error with GE data

Issue - State: closed - Opened by tsalo over 1 year ago - 18 comments
Labels: bug

#302 - Improve contributing and installation documentation

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: documentation

#301 - Fix nibabel import

Pull Request - State: closed - Opened by tsalo over 1 year ago - 5 comments
Labels: bug

#300 - AttributeError: module 'nibabel' has no attribute 'processing'

Issue - State: closed - Opened by Luoyu-Wang over 1 year ago - 3 comments
Labels: bug

#299 - Replace niworkflows calls with dependency calls (second attempt)

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: refactor

#298 - Replace weighted average with general kinetic model for multi-PLD data

Issue - State: open - Opened by tsalo over 1 year ago - 2 comments
Labels: enhancement

#297 - Get surface projection working

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#296 - Look into using SynthSeg for segmentation

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#295 - Use scan- or subject-wise hematocrit values, when available, to calculate T1blood

Issue - State: open - Opened by tsalo over 1 year ago
Labels: enhancement, discussion

#294 - Remove multi-echo elements

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: refactor

#293 - Make it clear that BIDS datasets should already be scaled

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: documentation

#292 - Document M0 scaling

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: documentation, testing

#291 - Raise warning if GE metadata does not match expected values from product sequence

Issue - State: open - Opened by tsalo over 1 year ago
Labels: enhancement, discussion

#290 - Adjust M0 to better match blood equilibrium magnetization

Issue - State: open - Opened by tsalo over 1 year ago
Labels: enhancement

#289 - Add example data and tutorial to documentation

Issue - State: open - Opened by tsalo over 1 year ago - 1 comment
Labels: documentation

#288 - Allow preprocessing without T1w scan

Issue - State: open - Opened by tsalo over 1 year ago
Labels: enhancement, discussion

#287 - Investigate "surround" or "sinc" subtraction

Issue - State: open - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement, discussion

#286 - Improve plots

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: documentation

#285 - Generate figures/report for the aggregated QC metrics from the combine-qc command

Issue - State: open - Opened by tsalo over 1 year ago - 2 comments
Labels: enhancement, discussion

#284 - Add histograms of CBF values by tissue type to report

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#283 - Use quantitative T1 map when available

Issue - State: open - Opened by tsalo over 1 year ago
Labels: enhancement, discussion

#282 - Reorganize atlases and add them to the package data

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug

#281 - Path error

Issue - State: closed - Opened by Jian-uon over 1 year ago - 4 comments
Labels: bug

#280 - Shift PostLabelingDelay(s) by slice times

Pull Request - State: closed - Opened by tsalo over 1 year ago - 2 comments
Labels: enhancement

#279 - Support runs with SCORE/SCRUB disabled

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug

#278 - SCORE/SCRUB disabled

Issue - State: closed - Opened by Jian-uon over 1 year ago - 6 comments
Labels: bug

#277 - Improve CBF figure settings

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#276 - Fix RTD build

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: documentation, ignore-for-release

#275 - Perform motion correction separately for each image type

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#274 - Remove test-made nifti files before storing artifacts

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: testing

#273 - Don't upload nifti artifacts to CircleCI

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: testing

#272 - Re-enable multi-PLD PASL support

Issue - State: open - Opened by tsalo over 1 year ago - 7 comments
Labels: enhancement, discussion

#271 - Remove unused workflows

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

#270 - Refactor more

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

#269 - Remove slice-timing correction

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug, breaking-change

#268 - Support single-PLD Q2TIPS PASL and multi-PLD PCASL

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#267 - Disable slice timing correction

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#266 - Implement zig-zag regression for motion correction

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

#265 - ASL reference image for GE data may be 4D

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: bug

#264 - Refactor more

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: refactor

#263 - Use same TPM threshold for GE and non-GE data

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug, breaking-change

#262 - aslprep 0.3.0 trying to download tpls

Issue - State: closed - Opened by dmd over 1 year ago - 13 comments
Labels: documentation, question

#261 - Refactor workflow connections

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: refactor

#260 - Why is TPM threshold for GE data different from threshold for non-GE data?

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: question

#259 - Investigate multi-echo ASL

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: maintenance

#258 - Prepare for 0.3.0 release

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: ignore-for-release, maintenance

#257 - Remove "mean" from mean CBF filenames and add "timeseries" to 4D CBF filenames

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: breaking-change

#256 - Refactor confounds and QC metrics

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: refactor

#255 - Ignore test_data folder

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: ignore-for-release, testing

#254 - Parallelize parcellation and replace atlases

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: breaking-change, refactor

#253 - Refactor SCORE/SCRUB and BASIL

Pull Request - State: open - Opened by tsalo over 1 year ago - 1 comment
Labels: refactor

#252 - Index aslcontext rows with "cbf", not "CBF"

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: bug

#251 - Support Q2TIPS data

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#250 - Re-enable multi-PLD PCASL support

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#249 - FD (and other confound) NaNs at end of confounds file

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: bug

#248 - Disable SCORE/SCRUB for GE/short runs and get GE workflow working

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: bug, breaking-change, testing

#247 - Parallelize across atlases and resolutions

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: refactor

#246 - Collect associated files at beginning of workflow

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

#245 - Replace RepetitionTime with RepetitionTimePreparation

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: bug

#244 - Estimate labeling efficiency based on ASL type and number of background suppression pulses

Pull Request - State: closed - Opened by tsalo over 1 year ago
Labels: enhancement

#243 - Hardcode T1blood for some field strengths and use Zhang 2013 formula for others

Pull Request - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: enhancement

GitHub / PennLINC/aslprep issues and pull requests