DCAN-Labs BIBSnet issues

DCAN-Labs / BIBSnet

This BIDS App provides the utility of creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model. It can easily be included in other processing pipelines and for circumventing JLF within Nibabies.

https://bibsnet.readthedocs.io/en/latest/

Apache License 2.0

4 stars 8 forks source link

issues

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Use SynthStrip-derived brainmask instead of current aseg-derived brainmask

#142 LuciMoore opened 2 weeks ago
0
Home directory in Docker now fully accessible

#141 joey-scanga opened 1 month ago
1
Deal with WARNING messages output at top of logs in some way so that they don't confuse users

#140 LuciMoore opened 1 month ago
1
Output nnU-Net inference/prediction routines as derivatives

#139 LuciMoore opened 1 month ago
0
permission error while using the latest image.

#138 scott-huberty closed 1 month ago
8
nnUNet failed to complete, exitcode -9

#137 dnkennedy closed 1 month ago
16
Remove flags not included in ReadTheDocs from usage

#136 LuciMoore opened 1 month ago
0
Add test data

#135 LuciMoore closed 1 week ago
3
FIX: extend read/execute permissions to all files used by BIBSnet

#134 scott-huberty closed 1 month ago
6
RuntimeError: Could not find a task with the ID (540)

#133 scott-huberty closed 1 month ago
1
Permissions error using singularity with latest image (3.4.x)

#132 scott-huberty closed 1 month ago
2
Use GitHub Actions to automatically update version number in Dockerfile

#131 LuciMoore opened 2 months ago
0
Suggestions for tar.gz stored on MSI s3

#130 LuciMoore opened 2 months ago
0
Rtd dev

#129 LuciMoore closed 2 months ago
0
Merge pull request #127 from DCAN-Labs/rtd_dev

#128 LuciMoore closed 2 months ago
0
Rtd dev

#127 LuciMoore closed 2 months ago
0
Update usage.md

#126 LuciMoore closed 2 months ago
0
Luci dev

#125 LuciMoore closed 2 months ago
0
Overcrop

#124 LuciMoore closed 2 months ago
0
add txonly to get_args

#123 LuciMoore closed 2 months ago
0
merge recent updates from main

#122 LuciMoore closed 2 months ago
0
fix for brain mask file name issue

#121 lundq163 closed 2 months ago
0
Recent change to the name of output mask files

#120 erikglee closed 2 months ago
2
Figure out more elegant solution for handling files used in multiple stages of the pipeline

#119 LuciMoore opened 3 months ago
0
Update stages.md

#118 LuciMoore closed 3 months ago
0
Many questions...

#117 dnkennedy closed 2 months ago
2
Run make aseg-derived mask function only once in postbibsnet

#116 LuciMoore closed 2 months ago
1
Update Dockerfile

#115 lundq163 closed 4 months ago
0
Remove chirality correction from postbibsnet

#114 LuciMoore closed 2 months ago
0
Update Dockerfile

#113 madisoth closed 4 months ago
0
Rm cc

#112 LuciMoore closed 4 months ago
0
Update Dockerfile

#111 lundq163 closed 4 months ago
0
Clarification on GPU Requirement

#110 scott-huberty closed 2 months ago
2
FYI: submitted to be included in the bids-apps registry

#109 yarikoptic opened 4 months ago
0
RuntimeError: Could not find a task with the ID 514

#108 shreyagudapati9 closed 2 months ago
9
Update postbibsnet.py

#107 erikglee closed 6 months ago
0
RC 3.2.0

#106 BarryTik closed 6 months ago
0
Use SynthStrip instead of fslmaths to create aseg-derived brainmask?

#105 LuciMoore closed 4 months ago
1
Clarify documentation on cropping/robustfov and possibly reduce flag redundancies

#104 LuciMoore closed 2 months ago
1
Fixed incorrect docker command, changed /out to /output

#103 joey-scanga closed 7 months ago
0
Update readthedocs

#102 LuciMoore closed 2 months ago
2
Denoise

#101 tikal004 closed 8 months ago
0
Add logic to help with frequent image overcropping

#100 LuciMoore closed 2 months ago
1
Iterative chirality correction

#99 LuciMoore closed 8 months ago
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 LuciMoore opened 9 months ago
0
Failure to skull strip / appropriately resize image

#97 kellyhi08 closed 9 months ago
4
Issue running BIBSnet through singularity

#96 kellyhi08 closed 9 months ago
8
Denoise

#95 tikal004 closed 10 months ago
0
Denoise

#94 tikal004 closed 10 months ago
0
Add more documentation on how brain-z-size is calculated

#93 LuciMoore closed 2 months ago
1