Closed jcohenadad closed 1 year ago
Reading the rest of the code I also notice a lot of "CT" references, ex:
Who introduced it and why? We never worked with CT data
Reading the rest of the code I also notice a lot of "CT" references. Who introduced it and why? We never worked with CT data
That would be me! When integrating the new loader pipeline back in March, we had 1 project using CT-scan (it was one of @andreanne-lemay project). It was added in PR #721.
CT-scan is not part of BIDS yet but there is a BEP in-progress for it: https://bids.neuroimaging.io/bep024 To accommodate CT, we used the same trick as with microscopy which is to "force index" the files and use a custom config for pybids.
can be mistaken for "extension for CT images", whereas it refers to MRI (nifti) images. Why the name 'ct'?
All the code lines you are referring to above are there to force the indexation of the files, even though they are not BIDS-compliant. At the moment, the extension for the CT files in the BEP are indeed NifTI, and ext_ct
truly means "extension for CT images".
We also have tests for it (in PR #725) along with a testing dataset (https://github.com/ivadomed/data-testing/pull/13).
Thank you @mariehbourget, I figured out after running the debugger that it was not a typo (I thought that someone wrote "CT" but was thinking "MRI" instead), but that the part common to all modalities (including MRI) comes later:
I will suggest some comments to clarify the code for someone not familiar with BIDS (I am familiar with BIDS but was nevertheless confused about this chunk of code, why we have sections with microscopy/CT and not with MRI, etc.).
Comments are currently a little bit above here: https://github.com/ivadomed/ivadomed/blob/d1b9e118f491d9e5e88523f8d0f0cae65b26ecca/ivadomed/loader/bids_dataframe.py#L80-L85
But I would be happy to review them to make it clearer.
yes, i did see the comments but it didn't help me 😅 . I'll suggest something
@jcohenadad,
Update on this issue:
I worked on removing force-indexing of micr
files in PR #1203. While doing that, I made some clarifications to better explain how and why we are force-indexing ct
files, if you are interested in reviewing.
The variable
ext_ct
:https://github.com/ivadomed/ivadomed/blob/d1b9e118f491d9e5e88523f8d0f0cae65b26ecca/ivadomed/loader/bids_dataframe.py#L86-L87
can be mistaken for "extension for CT images", whereas it refers to MRI (nifti) images. Why the name 'ct'?