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
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Recent change to the name of output mask files #120

Closed erikglee closed 2 months ago

erikglee commented 2 months ago

What happened?

Hello, I am looking at the outputs from a new version of the Bibsnet container (release-3.4.0) and it seems like one of the files is named differently than what I have previously encountered. I have pasted the old/new file names below. For reference, it is just this single nifti file that has a new file name. The JSON that corresponds with this nifti still has a naming pattern that matches with the old naming schema. I am guessing this is a bug, so wanted to let you know!

Old file name: sub-102283_ses-V02_space-T2w_desc-brain_mask.nii.gz New file name: sub-102283_ses-V02_space-T2w_desc-aseg_dseg_T2_mask.nii.gz

What command did you use?

singularity run bibsnet.sif /in /out participant

What version of BIBSnet are you using?

release-3.4.0

Directory Structure

No response

Relevant log output

No response

Add any additional information or context about the problem here.

No response

scott-huberty commented 2 months ago

I've noticed this too.

It looks the nifti filename is generated here (the new naming scheme):

https://github.com/DCAN-Labs/BIBSnet/blob/ace7a360b19507573e48c14024442f354b2289ec/src/postbibsnet.py#L116-L118

After searching with git grep it appears that this new naming scheming was introduced a while ago in #51, and then moved to postbibsnet.py in #83 , where it lives now.

For what it is worth, The docs still refer to the "old" naming scheme, when describing BIBSnet outputs.

@erikglee I'm not sure if you were just using a really old version of BIBSnet, or if something changed in the code base that makes BIBsnet hit that aforementioned line for your file, when it didn't before?

LuciMoore commented 2 months ago

Resolved in release 3.4.1 by https://github.com/DCAN-Labs/BIBSnet/pull/121