DCAN-Labs/BIBSnet

Issues

• Deal with WARNING messages output at top of logs in some way so that they don't confuse users

  #140 opened a month ago by LuciMoore
  1

• Suggestions for tar.gz stored on MSI s3

  #130 opened 2 months ago by LuciMoore
  0

• permission error while using the latest image.

  #138 opened a month ago by scott-huberty
  8

• nnUNet failed to complete, exitcode -9

  #137 opened 2 months ago by dnkennedy
  16

• Test possible bugs with --overwrite flag & possibly default to clearing old outputs until this is resolved

  #44 opened a year ago by LuciMoore
  3

• Output nnU-Net inference/prediction routines as derivatives

  #139 opened 2 months ago by LuciMoore
  0

• Permissions error using singularity with latest image (3.4.x)

  #132 opened 2 months ago by scott-huberty
  2

• Add test data

  #135 opened 2 months ago by LuciMoore
  1

• RuntimeError: Could not find a task with the ID 514

  #108 opened 2 months ago by shreyagudapati9
  9

• Remove flags not included in ReadTheDocs from usage

  #136 opened 2 months ago by LuciMoore
  0

• RuntimeError: Could not find a task with the ID (540)

  #133 opened 2 months ago by scott-huberty
  1

• Use GitHub Actions to automatically update version number in Dockerfile

  #131 opened 2 months ago by LuciMoore
  0

• Many questions...

  #117 opened 2 months ago by dnkennedy
  2

• Repository Data Directory

  #42 opened 2 months ago by audreymhoughton
  1

• Minor bug when running BIBSNet without overwrite flag when there are partial existing intermediate outputs in tmp space

  #46 opened 2 months ago by LuciMoore
  1

• postBIBSnet chirality correction not accurate around midline

  #84 opened 2 months ago by moser297
  4

• Update readthedocs

  #102 opened 2 months ago by LuciMoore
  2

• Clarification on GPU Requirement

  #110 opened 2 months ago by scott-huberty
  2

• Recent change to the name of output mask files

  #120 opened 2 months ago by erikglee
  2

• Clarify documentation on cropping/robustfov and possibly reduce flag redundancies

  #104 opened 3 months ago by LuciMoore
  1

• Add logic to help with frequent image overcropping

  #100 opened 3 months ago by LuciMoore
  1

• Add more documentation on how brain-z-size is calculated

  #93 opened 3 months ago by LuciMoore
  1

• Run make aseg-derived mask function only once in postbibsnet

  #116 opened 3 months ago by LuciMoore
  1

• Error downloading FSL in Docker build

  #85 opened 3 months ago by tikal004
  3

• Is the T2-only Model flag up and running?

  #77 opened 3 months ago by henrycikanek
  4

• Rename S3 data archive to s3://bibsnet-data

  #89 opened 3 months ago by tikal004
  1

• Issue running prebibsnet and bibsnet stages, then later running postbibsnet

  #87 opened 3 months ago by erikglee
  1

• Figure out more elegant solution for handling files used in multiple stages of the pipeline

  #119 opened 3 months ago by LuciMoore
  0

• Remove unused files from data.tar.gz

  #90 opened 3 months ago by LuciMoore
  1

• Use SynthStrip instead of fslmaths to create aseg-derived brainmask?

  #105 opened 4 months ago by LuciMoore
  1

• FYI: submitted to be included in the bids-apps registry

  #109 opened 5 months ago by yarikoptic
  0

• Add fslorient to check orientation and either exit with error if orientation/header info is non-compatible with BIBSNet utilities or use fslorient2std to make compatible

  #98 opened 9 months ago by LuciMoore
  0

• Failure to skull strip / appropriately resize image

  #97 opened 9 months ago by kellyhi08
  4

• Issue running BIBSnet through singularity

  #96 opened 10 months ago by kellyhi08
  8

• Turn off post-processing settings for cases where manual segmentation correction has been performed

  #92 opened a year ago by erikglee
  2

• Run Nibabies + XCP-D

  #66 opened a year ago by audreymhoughton
  1

• Generated only one half of the aseg file

  #75 opened a year ago by yanbin-niu
  4

• Document T1-only / T2-only

  #68 opened a year ago by audreymhoughton
  0

• Incorporate Model 552

  #70 opened a year ago by audreymhoughton
  0

• Question link is wrong

  #71 opened a year ago by rosemccollum
  0

• Error when running model 515 - T2w-only

  #65 opened a year ago by audreymhoughton
  9

• Issues with Segmentation File

  #59 opened a year ago by henrycikanek
  3

• Dataset_description.json error

  #58 opened a year ago by ajdneuro
  4

• Exactly one BIBSnet seg file

  #57 opened a year ago by ajdneuro
  3

• T2 images rotated during T2 to T1 alignment in preBIBSNet

  #50 opened a year ago by moser297
  3

• Output a separate segmentation in native T2w space (in addition to current output in T1w space)

  #45 opened a year ago by LuciMoore
  1

• CABINET is having an issue converting 6 month aged subjects to int

  #54 opened a year ago by henrycikanek
  4

• Issues with Segmentation and Surfaces Generated from BIBSNET

  #47 opened a year ago by henrycikanek
  5

• Read only file system error

  #43 opened a year ago by ajdneuro
  9

• Make aseg-derived mask only once

  #48 opened a year ago by LuciMoore
  0