PennLINC/qsiprep issues and pull requests

#447 - Various `autorecon` errors

Issue - State: closed - Opened by dyhan316 about 2 years ago - 1 comment

#447 - Various `autorecon` errors

Issue - State: closed - Opened by dyhan316 about 2 years ago - 1 comment

#446 - questions about QSIprep 12.1 flow description

Issue - State: closed - Opened by WilliamFCB about 2 years ago - 7 comments

#444 - from qsiprep.cli.run import main ModuleNotFoundError: No module named 'qsiprep.cli'

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

#442 - Add more explicit tests for bundles

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

#438 - Error loading yml plugin using 0.16.ORc3

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

#436 - [WIP] ENH: Add TractSeg reconstruction

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

#435 - [WIP] ENH: Add SIFT-classic

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

#434 - [WIP] ENH: Export_All in pyafq

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

#434 - [WIP] ENH: Export_All in pyafq

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

#432 - Bug in QSIPREP reconstruction pipeline when using --dwi-only

Issue - State: closed - Opened by julfou81 over 2 years ago - 7 comments

#432 - Bug in QSIPREP reconstruction pipeline when using --dwi-only

Issue - State: closed - Opened by julfou81 over 2 years ago - 7 comments

#431 - [feature request] SIFT1

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

#429 - [ENH] optimize connectome2tck

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

#424 - BrokenProcessPool

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

#423 - Connectivity on Gordon333

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

#422 - WIP: [ENH] Pyafq visualization of the recognized bundles for reportlets

Pull Request - State: closed - Opened by 36000 over 2 years ago - 18 comments

#421 - PyAFQ QC report

Issue - State: closed - Opened by 36000 over 2 years ago - 3 comments

#415 - matrix files - missing data

Issue - State: closed - Opened by hbyrne17 over 2 years ago - 3 comments

#414 - Fixes typos on FreeSurfer requirements for ss3t hsvs recon

Pull Request - State: closed - Opened by pcamach2 over 2 years ago - 1 comment

#413 - QSIPrep not combining same-session dwi scans

Issue - State: closed - Opened by pmd84 over 2 years ago - 11 comments

#412 - QSIprep recon_only is stuck at "plot_connectivity"

Issue - State: closed - Opened by dyhan316 over 2 years ago - 3 comments

#411 - Reorienting to FSL

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

#410 - Session biases

Issue - State: open - Opened by GalKepler over 2 years ago - 3 comments

#408 - Node t1_2_mni failed to run

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

#407 - Cannot run qsiprep. Missing dependencies: fugue, prelude

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

#402 - estimate_fod failed to run

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

#400 - AMICO sort of failing

Issue - State: open - Opened by araikes over 2 years ago - 3 comments

#395 - ModuleNotFoundError: No module named 'sklearn.metrics.regression'

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

#393 - [FIX] Properly transform the 4D CNR images from Eddy

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

#391 - [ENH] Add RecoBundles/BUAN workflow

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

#390 - DWIs not found for dHCP data

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

#389 - Patch2Self after Eddy/ SHORELine

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

#388 - Boilerplate question

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

#385 - Processing HCP-like dataset

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

#384 - --do-reconall doesn't seem to work in v 0.15.x

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

#383 - [ENH] Auto size step size based on voxel size

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

#378 - no figures included in HTML report

Issue - State: open - Opened by giulia-berto over 2 years ago - 12 comments

#378 - no figures included in HTML report

Issue - State: open - Opened by giulia-berto over 2 years ago - 11 comments

#374 - "Original files don't match"

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

#373 - ABCD DWI Data Not Recognised

Issue - State: closed - Opened by AlicjaMonaghan over 2 years ago - 8 comments

#371 - [FIX] spelling and fix defaults

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

#370 - Qsiprep recon mrtrix seeding

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

#369 - QSIPrep does distortion correction with different PE directions?

Issue - State: closed - Opened by akelkar26 over 2 years ago - 2 comments

#369 - QSIPrep does distortion correction with different PE directions?

Issue - State: closed - Opened by akelkar26 over 2 years ago - 2 comments

#368 - [ENH] add n_procs to recon nodes

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

#367 - DKI Setup

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

#366 - [ENH] Add DKI

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

#365 - selected_for_topup missing from confounds.tsv

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

#364 - [ENH] make ODF plots optional

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

#363 - [FIX] capitalization of ABCD gradient data

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

#359 - Exception raised while executing Node concat

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

#352 - [ENH] Add back a dsi studio recon test

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

#342 - Documentation sentence ends abruptly

Issue - State: open - Opened by arokem over 2 years ago - 1 comment
Labels: documentation

#339 - Bad slices in qsiprep processed data

Issue - State: closed - Opened by WilliamFCB over 2 years ago - 10 comments

#329 - QSIPrep failed: Workflow did not execute cleanly

Issue - State: closed - Opened by barisgenc12 almost 3 years ago - 7 comments

#326 - Error with eddy_cuda with option -repol

Issue - State: closed - Opened by julfou81 almost 3 years ago - 2 comments

#324 - issue when using "method":"lsr" with eddy

Issue - State: closed - Opened by julfou81 almost 3 years ago - 2 comments

#323 - Standalone SHORELine motion correction

Issue - State: closed - Opened by araikes almost 3 years ago - 1 comment

#322 - --write-local-bvecs flag does not work as expected

Issue - State: closed - Opened by amyhegarty almost 3 years ago

#321 - --prefer-dedicated-fmaps option doesn't work as expected

Issue - State: closed - Opened by lucindasisk almost 3 years ago - 7 comments

#318 - QSIPrep derivative datasets are not (py)BIDS compliant

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

#317 - Problem with mrtrix_singleshell_ss3t

Issue - State: closed - Opened by zhangxiaobai12345 almost 3 years ago - 1 comment

#314 - [ENH] add datasink for acpc transform

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

#313 - Transformation from original T1w to qsiprep space

Issue - State: closed - Opened by Giuseppe1988 almost 3 years ago

#311 - Parallel Processing

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

#310 - Two anat directories created - v0.14.3

Issue - State: closed - Opened by kodiweera almost 3 years ago - 1 comment

#309 - [feature request] final gradient files from dwigradcheck

Issue - State: open - Opened by smeisler almost 3 years ago - 1 comment

#303 - [ENH] Add pyafq

Pull Request - State: closed - Opened by mattcieslak about 3 years ago - 12 comments

#302 - [ENH] Add PyAFQ reconstruction workflow

Issue - State: closed - Opened by mattcieslak about 3 years ago - 1 comment

#298 - [FEATURE REQUEST] Saving Eddy-outputs in output folder for use in EddyQC

Issue - State: open - Opened by ajschadler12 about 3 years ago - 19 comments

#298 - [FEATURE REQUEST] Saving Eddy-outputs in output folder for use in EddyQC

Issue - State: open - Opened by ajschadler12 about 3 years ago - 19 comments

#296 - [DOC] ss3t_csd_beta1 needs better documentation

Issue - State: open - Opened by layerConnectome about 3 years ago - 3 comments

#290 - cannot track output of --out_assignments in tck2connectome

Issue - State: closed - Opened by sebnaze about 3 years ago - 10 comments

#288 - output folder-qsirecon only have logs folder

Issue - State: closed - Opened by JING-797 about 3 years ago - 1 comment

#284 - The output FA image shows too many high value spots

Issue - State: closed - Opened by aghayoor about 3 years ago - 2 comments

#283 - Custom atlas in T1w space

Issue - State: closed - Opened by Giuseppe1988 about 3 years ago - 5 comments

#282 - Specify a session for QSIPrep to process

Issue - State: closed - Opened by meet10may about 3 years ago - 1 comment

#277 - Fails to find DWI pairs

Issue - State: closed - Opened by aghayoor about 3 years ago - 15 comments

#276 - Using Lesion Map with ACT/5ttgen/5ttedit

Issue - State: closed - Opened by m-petersen about 3 years ago - 2 comments

#275 - QSIprep Mac - nothing happens

Issue - State: closed - Opened by dubergonzoni about 3 years ago - 4 comments

#274 - qsiprep output owned by root

Issue - State: closed - Opened by treanus about 3 years ago - 2 comments

#271 - [FIX] Fieldmap bug when using datalad

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

#270 - ENH: Clarifying Documentation

Pull Request - State: closed - Opened by TinasheMTapera about 3 years ago - 1 comment

#268 - [ENH] Ingress HCP preprocessed data

Pull Request - State: closed - Opened by mattcieslak about 3 years ago - 1 comment

#262 - subject html file doesn't have any visual reports like carpet plots!!

Issue - State: open - Opened by M31glx over 3 years ago - 31 comments

#262 - subject html file doesn't have any visual reports like carpet plots!!

Issue - State: open - Opened by M31glx over 3 years ago - 31 comments

#259 - build an only-track pipeline with other algorithm after reconstruction

Issue - State: closed - Opened by weiwei-wch over 3 years ago

#258 - Add qsiprep_group_report for dmriprep-viewer

Pull Request - State: closed - Opened by j-bourque over 3 years ago

#255 - Rename Denoising in Report Generated

Issue - State: open - Opened by ShreyasFadnavis over 3 years ago - 1 comment

#237 - Reading Transforms output by qsiprep in python

Issue - State: closed - Opened by 36000 over 3 years ago - 2 comments

#235 - What would I do with qsiprep-singularity?

Issue - State: closed - Opened by kodiweera over 3 years ago - 1 comment

#225 - ValueError: Field of view of image #1 is different from reference FOV

Issue - State: open - Opened by IRuotsa over 3 years ago - 9 comments

#225 - ValueError: Field of view of image #1 is different from reference FOV

Issue - State: open - Opened by IRuotsa over 3 years ago - 9 comments

#223 - [ENH] Make recon workflows correctly process dwi-only inputs

Pull Request - State: closed - Opened by mattcieslak over 3 years ago - 1 comment

GitHub / PennLINC/qsiprep issues and pull requests